1
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Wang N, Zhao Q, Huang Y, Wen C, Li Y, Bao M, Wu L. Lnc-TMEM132D-AS1 as a potential therapeutic target for acquired resistance to osimertinib in non-small-cell lung cancer. Mol Omics 2023; 19:238-251. [PMID: 36651104 DOI: 10.1039/d2mo00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Acquired resistance is a major obstacle to the therapeutic efficacy of osimertinib in non-small-cell lung cancer (NSCLC). Current knowledge about the role of long non-coding RNAs (lncRNAs) in this phenomenon is insufficient. In this study, we screened the differentially expressed lncRNAs between osimertinib-sensitive and -resistant NSCLC cell lines, and determined that lnc-TMEM132D-AS1 was significantly upregulated in osimertinib-resistant NSCLC cells, as well as in the plasma of osimertinib-resistant NSCLC patients. Lnc-TMEM132D-AS1 markedly decreased the osimertinib sensitivity of NSCLC cells. After osimertinib exposure, it increased the cell proliferation and colony formation, decreased the cell apoptosis, and induced M2/G-phase cell cycle arrest. After identifying its cytoplasmic localization, a functional lnc-TMEM132D-AS1-miRNA-mRNA interaction network and a protein-protein interaction (PPI) network were constructed to analyze its putative target genes and biological functions. Lnc-TMEM132D-AS1 could directly bind to miR-766-5p and lead to the upregulation of ectonucleoside triphosphate diphosphohydrolase-1 (ENTPD1), resulting in an increase in cell proliferation. Moreover, upregulated ENTPD1 was also associated with enhanced tumor infiltration of immunosuppressive cells and poor prognosis in NSCLC patients. In summary, lnc-TMEM132D-AS1 plays a crucial role in osimertinib resistance. It may serve as a prognostic biomarker and a potential therapeutic target for acquired resistance to osimertinib in NSCLC.
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Affiliation(s)
- Nan Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
| | - Qilin Zhao
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yutang Huang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
| | - Chunjie Wen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
| | - Yaji Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
| | - Meihua Bao
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, 410219, China.,Academician Workstation, Changsha Medical University, Changsha, 410219, China
| | - Lanxiang Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China. .,Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, China
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2
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Ferreira D, Soares M, Correia J, Adega F, Ferreira F, Chaves R. Satellite Noncoding RNAs (ncRNA) as Cancer Biomarkers? New Insights from FA-SAT ncRNA Molecular and Clinical Profiles in Feline Mammary Tumors. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:622-632. [PMID: 36342778 DOI: 10.1089/omi.2022.0114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Satellite noncoding RNAs (ncRNAs) are a new frontier of cancer biology research and biomarkers. While the knowledge on ncRNAs in human cancers is still limited, studies in other species can be informative to guide future translational research and development for cancer molecular targets and diagnostics. In this context, FA-SAT is the major satellite DNA of the cat genome, which is also present in humans, being transcribed in both species. In this study, we report new insights on FA-SAT (DNA and RNA) profile in feline mammary tumors, using disease-free tissues from the same animals as reference. We quantified the FA-SAT DNA and RNA levels (long and small transcripts) by real-time quantitative polymerase chain reaction (qPCR) and RT-qPCR. The comparison of the FA-SAT DNA and RNA levels with clinicopathological parameters revealed several associations, such as (1) the FA-SAT DNA levels' positive relation with lymphovascular invasion, (2) the FA-SAT long RNA negative correlation with Ki-67 index, and its positive association with Estrogen Receptor status, and (3) the FA-SAT small RNA level positive correlation with tumor size and skin ulceration. Also, FA-SAT long RNA is correlated with ERBB2 and c-MYC RNA levels. These data collectively suggest that FA-SAT ncRNA offers prospects as a potential cancer biomarker in cats. Further studies in humans are also needed to decipher the emerging role of ncRNAs in cancer biology and precision medicine fields. This work brings new information on the relation of FA-SAT ncRNAs with the oncogenic process, uncovering a new potential cancer biomarker.
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Affiliation(s)
- Daniela Ferreira
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Maria Soares
- IUEM, Instituto Universitário Egas Moniz, Egas Moniz-Cooperativa de Ensino Superior, CRL, Caparica, Portugal
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Jorge Correia
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Filomena Adega
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Fernando Ferreira
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Raquel Chaves
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
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3
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Arunkumar G, Baek S, Sturgill D, Bui M, Dalal Y. Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells. SCIENCE ADVANCES 2022; 8:eabl5621. [PMID: 35235361 PMCID: PMC8890707 DOI: 10.1126/sciadv.abl5621] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Chromosome instability is a critical event in cancer progression. Histone H3 variant CENP-A plays a fundamental role in defining centromere identity, structure, and function but is innately overexpressed in several types of solid cancers. In the cancer background, excess CENP-A is deposited ectopically on chromosome arms, including 8q24/cMYC locus, by invading transcription-coupled H3.3 chaperone pathways. Up-regulation of lncRNAs in many cancers correlates with poor prognosis and recurrence in patients. We report that transcription of 8q24-derived oncogenic lncRNAs plays an unanticipated role in altering the 8q24 chromatin landscape by H3.3 chaperone-mediated deposition of CENP-A-associated complexes. Furthermore, a transgene cassette carrying specific 8q24-derived lncRNA integrated into a naïve chromosome locus recruits CENP-A to the new location in a cis-acting manner. These data provide a plausible mechanistic link between locus-specific oncogenic lncRNAs, aberrant local chromatin structure, and the generation of new epigenetic memory at a fragile site in human cancer cells.
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4
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Trotter M, Harris C, Cloutier M, Samanta M, Kalantry S. Highly Resolved Detection of Long Non-coding RNAs In Situ. Methods Mol Biol 2021; 2372:123-144. [PMID: 34417748 DOI: 10.1007/978-1-0716-1697-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been postulated to function in a number of DNA-based processes, most notably transcription. The detection of lncRNAs in situ can offer insights into their function. Fluorescence in situ hybridization (FISH) enables the detection of specific nucleic acid sequences, including lncRNAs, within individual cells. Current RNA FISH techniques can inform both the localization and expression level of RNA transcripts. Together with advances in microscopy, these in situ techniques now allow for visualization and quantification of even lowly expressed or unstable lncRNAs. When combined with detection of associated proteins and chromatin modifications by immunofluorescence, RNA FISH can lend essential insights into lncRNA function. Here, we describe an integrated set of protocols to detect, individually or in combination, specific RNAs, DNAs, proteins, and histone modifications in single cells at high sensitivity using conventional fluorescence microscopy.
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Affiliation(s)
- Megan Trotter
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48105-1536, MI, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48105-1536, MI, USA
| | - Marissa Cloutier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48105-1536, MI, USA
| | - Milan Samanta
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48105-1536, MI, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48105-1536, MI, USA.
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5
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Matveevsky S, Tretiakov A, Kashintsova A, Bakloushinskaya I, Kolomiets O. Meiotic Nuclear Architecture in Distinct Mole Vole Hybrids with Robertsonian Translocations: Chromosome Chains, Stretched Centromeres, and Distorted Recombination. Int J Mol Sci 2020; 21:E7630. [PMID: 33076404 PMCID: PMC7589776 DOI: 10.3390/ijms21207630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/13/2020] [Indexed: 11/24/2022] Open
Abstract
Genome functioning in hybrids faces inconsistency. This mismatch is manifested clearly in meiosis during chromosome synapsis and recombination. Species with chromosomal variability can be a model for exploring genomic battles with high visibility due to the use of advanced immunocytochemical methods. We studied synaptonemal complexes (SC) and prophase I processes in 44-chromosome intraspecific (Ellobius tancrei × E. tancrei) and interspecific (Ellobius talpinus × E. tancrei) hybrid mole voles heterozygous for 10 Robertsonian translocations. The same pachytene failures were found for both types of hybrids. In the intraspecific hybrid, the chains were visible in the pachytene stage, then 10 closed SC trivalents formed in the late pachytene and diplotene stage. In the interspecific hybrid, as a rule, SC trivalents composed the SC chains and rarely could form closed configurations. Metacentrics involved with SC trivalents had stretched centromeres in interspecific hybrids. Linkage between neighboring SC trivalents was maintained by stretched centromeric regions of acrocentrics. This centromeric plasticity in structure and dynamics of SC trivalents was found for the first time. We assume that stretched centromeres were a marker of altered nuclear architecture in heterozygotes due to differences in the ancestral chromosomal territories of the parental species. Restructuring of the intranuclear organization and meiotic disturbances can contribute to the sterility of interspecific hybrids, and lead to the reproductive isolation of studied species.
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Affiliation(s)
- Sergey Matveevsky
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Artemii Tretiakov
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Anna Kashintsova
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Irina Bakloushinskaya
- Laboratory of Genome Evolution and Mechanisms of Speciation, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Oxana Kolomiets
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
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6
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Meiotic Chromosome Contacts as a Plausible Prelude for Robertsonian Translocations. Genes (Basel) 2020; 11:genes11040386. [PMID: 32252399 PMCID: PMC7230836 DOI: 10.3390/genes11040386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Robertsonian translocations are common chromosomal alterations. Chromosome variability affects human health and natural evolution. Despite the significance of such mutations, no mechanisms explaining the emergence of such translocations have yet been demonstrated. Several models have explored possible changes in interphase nuclei. Evidence for non-homologous chromosomes end joining in meiosis is scarce, and is often limited to uncovering mechanisms in damaged cells only. This study presents a primarily qualitative analysis of contacts of non-homologous chromosomes by short arms, during meiotic prophase I in the mole vole, Ellobius alaicus, a species with a variable karyotype, due to Robertsonian translocations. Immunocytochemical staining of spermatocytes demonstrated the presence of four contact types for non-homologous chromosomes in meiotic prophase I: (1) proximity, (2) touching, (3) anchoring/tethering, and (4) fusion. Our results suggest distinct mechanisms for chromosomal interactions in meiosis. Thus, we propose to change the translocation mechanism model from ‘contact first’ to ‘contact first in meiosis’.
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7
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O'Neill RJ. Seq'ing identity and function in a repeat-derived noncoding RNA world. Chromosome Res 2020; 28:111-127. [PMID: 32146545 PMCID: PMC7393779 DOI: 10.1007/s10577-020-09628-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 01/06/2023]
Abstract
Innovations in high-throughout sequencing approaches are being marshaled to both reveal the composition of the abundant and heterogeneous noncoding RNAs that populate cell nuclei and lend insight to the mechanisms by which noncoding RNAs influence chromosome biology and gene expression. This review focuses on some of the recent technological developments that have enabled the isolation of nascent transcripts and chromatin-associated and DNA-interacting RNAs. Coupled with emerging genome assembly and analytical approaches, the field is poised to achieve a comprehensive catalog of nuclear noncoding RNAs, including those derived from repetitive regions within eukaryotic genomes. Herein, particular attention is paid to the challenges and advances in the sequence analyses of repeat and transposable element-derived noncoding RNAs and in ascribing specific function(s) to such RNAs.
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Affiliation(s)
- Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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8
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Smalec BM, Heider TN, Flynn BL, O'Neill RJ. A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive. Chromosome Res 2019; 27:237-252. [PMID: 30771198 PMCID: PMC6733818 DOI: 10.1007/s10577-019-09605-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/26/2019] [Accepted: 01/29/2019] [Indexed: 12/17/2022]
Abstract
A common feature of eukaryotic centromeres is the presence of large tracts of tandemly arranged repeats, known as satellite DNA. However, these centromeric repeats appear to experience rapid evolution under forces such as molecular drive and centromere drive, seemingly without consequence to the integrity of the centromere. Moreover, blocks of heterochromatin within the karyotype, including the centromere, are hotspots for chromosome rearrangements that may drive speciation events by contributing to reproductive isolation. However, the relationship between the evolution of heterochromatic sequences and the karyotypic dynamics of these regions remains largely unknown. Here, we show that a single conserved satellite DNA sequence in the order Rodentia of the genus Peromyscus localizes to recurrent sites of chromosome rearrangements and heterochromatic amplifications. Peromyscine species display several unique features of chromosome evolution compared to other Rodentia, including stable maintenance of a strict chromosome number of 48 among all known species in the absence of any detectable interchromosomal rearrangements. Rather, the diverse karyotypes of Peromyscine species are due to intrachromosomal variation in blocks of repeated DNA content. Despite wide variation in the copy number and location of repeat blocks among different species, we find that a single satellite monomer maintains a conserved sequence and homogenized tandem repeat structure, defying predictions of molecular drive. The conservation of this satellite monomer results in common, abundant, and large blocks of chromatin that are homologous among chromosomes within one species and among diverged species. Thus, such a conserved repeat may have facilitated the retention of polymorphic chromosome variants within individuals and intrachromosomal rearrangements between species-both factors that have previously been hypothesized to contribute towards the extremely wide range of ecological adaptations that this genus exhibits.
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Affiliation(s)
- Brendan M Smalec
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Thomas N Heider
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Brianna L Flynn
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA.
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9
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Peng C, Han S, Zhang H, Li Y. RPITER: A Hierarchical Deep Learning Framework for ncRNA⁻Protein Interaction Prediction. Int J Mol Sci 2019; 20:E1070. [PMID: 30832218 PMCID: PMC6429152 DOI: 10.3390/ijms20051070] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play crucial roles in multiple fundamental biological processes, such as post-transcriptional gene regulation, and are implicated in many complex human diseases. Mostly ncRNAs function by interacting with corresponding RNA-binding proteins. The research on ncRNA⁻protein interaction is the key to understanding the function of ncRNA. However, the biological experiment techniques for identifying RNA⁻protein interactions (RPIs) are currently still expensive and time-consuming. Due to the complex molecular mechanism of ncRNA⁻protein interaction and the lack of conservation for ncRNA, especially for long ncRNA (lncRNA), the prediction of ncRNA⁻protein interaction is still a challenge. Deep learning-based models have become the state-of-the-art in a range of biological sequence analysis problems due to their strong power of feature learning. In this study, we proposed a hierarchical deep learning framework RPITER to predict RNA⁻protein interaction. For sequence coding, we improved the conjoint triad feature (CTF) coding method by complementing more primary sequence information and adding sequence structure information. For model design, RPITER employed two basic neural network architectures of convolution neural network (CNN) and stacked auto-encoder (SAE). Comprehensive experiments were performed on five benchmark datasets from PDB and NPInter databases to analyze and compare the performances of different sequence coding methods and prediction models. We found that CNN and SAE deep learning architectures have powerful fitting abilities for the k-mer features of RNA and protein sequence. The improved CTF coding method showed performance gain compared with the original CTF method. Moreover, our designed RPITER performed well in predicting RNA⁻protein interaction (RPI) and could outperform most of the previous methods. On five widely used RPI datasets, RPI369, RPI488, RPI1807, RPI2241 and NPInter, RPITER obtained A U C of 0.821, 0.911, 0.990, 0.957 and 0.985, respectively. The proposed RPITER could be a complementary method for predicting RPI and constructing RPI network, which would help push forward the related biological research on ncRNAs and lncRNAs.
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Affiliation(s)
- Cheng Peng
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China.
| | - Siyu Han
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China.
| | - Hui Zhang
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China.
| | - Ying Li
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China.
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10
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Smurova K, De Wulf P. Centromere and Pericentromere Transcription: Roles and Regulation … in Sickness and in Health. Front Genet 2018; 9:674. [PMID: 30627137 PMCID: PMC6309819 DOI: 10.3389/fgene.2018.00674] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/04/2018] [Indexed: 12/26/2022] Open
Abstract
The chromosomal loci known as centromeres (CEN) mediate the equal distribution of the duplicated genome between both daughter cells. Specifically, centromeres recruit a protein complex named the kinetochore, that bi-orients the replicated chromosome pairs to the mitotic or meiotic spindle structure. The paired chromosomes are then separated, and the individual chromosomes segregate in opposite direction along the regressing spindle into each daughter cell. Erroneous kinetochore assembly or activity produces aneuploid cells that contain an abnormal number of chromosomes. Aneuploidy may incite cell death, developmental defects (including genetic syndromes), and cancer (>90% of all cancer cells are aneuploid). While kinetochores and their activities have been preserved through evolution, the CEN DNA sequences have not. Hence, to be recognized as sites for kinetochore assembly, CEN display conserved structural themes. In addition, CEN nucleosomes enclose a CEN-exclusive variant of histone H3, named CENP-A, and carry distinct epigenetic labels on CENP-A and the other CEN histone proteins. Through the cell cycle, CEN are transcribed into non-coding RNAs. After subsequent processing, they become key components of the CEN chromatin by marking the CEN locus and by stably anchoring the CEN-binding kinetochore proteins. CEN transcription is tightly regulated, of low intensity, and essential for differentiation and development. Under- or overexpression of CEN transcripts, as documented for myriad cancers, provoke chromosome missegregation and aneuploidy. CEN are genetically stable and fully competent only when they are insulated from the surrounding, pericentromeric chromatin, which must be silenced. We will review CEN transcription and its contribution to faithful kinetochore function. We will further discuss how pericentromeric chromatin is silenced by RNA processing and transcriptionally repressive chromatin marks. We will report on the transcriptional misregulation of (peri)centromeres during stress, natural aging, and disease and reflect on whether their transcripts can serve as future diagnostic tools and anti-cancer targets in the clinic.
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Affiliation(s)
- Ksenia Smurova
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Peter De Wulf
- Centre for Integrative Biology, University of Trento, Trento, Italy
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11
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Chaves R, Ferreira D, Mendes-da-Silva A, Meles S, Adega F. FA-SAT Is an Old Satellite DNA Frozen in Several Bilateria Genomes. Genome Biol Evol 2018; 9:3073-3087. [PMID: 29608678 PMCID: PMC5714208 DOI: 10.1093/gbe/evx212] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2017] [Indexed: 12/17/2022] Open
Abstract
In recent years, a growing body of evidence has recognized the tandem repeat sequences, and specifically satellite DNA, as a functional class of sequences in the genomic “dark matter.” Using an original, complementary, and thus an eclectic experimental design, we show that the cat archetypal satellite DNA sequence, FA-SAT, is “frozen” conservatively in several Bilateria genomes. We found different genomic FA-SAT architectures, and the interspersion pattern was conserved. In Carnivora genomes, the FA-SAT-related sequences are also amplified, with the predominance of a specific FA-SAT variant, at the heterochromatic regions. We inspected the cat genome project to locate FA-SAT array flanking regions and revealed an intensive intermingling with transposable elements. Our results also show that FA-SAT-related sequences are transcribed and that the most abundant FA-SAT variant is not always the most transcribed. We thus conclude that the DNA sequences of FA-SAT and their transcripts are “frozen” in these genomes. Future work is needed to disclose any putative function that these sequences may play in these genomes.
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Affiliation(s)
- Raquel Chaves
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Daniela Ferreira
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Ana Mendes-da-Silva
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Susana Meles
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Filomena Adega
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
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12
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Klein SJ, O'Neill RJ. Transposable elements: genome innovation, chromosome diversity, and centromere conflict. Chromosome Res 2018; 26:5-23. [PMID: 29332159 PMCID: PMC5857280 DOI: 10.1007/s10577-017-9569-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
Abstract
Although it was nearly 70 years ago when transposable elements (TEs) were first discovered “jumping” from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive. Finally, we focus on the role of TEs in the establishment, maintenance, and stabilization of critical, yet rapidly evolving, chromosome features: eukaryotic centromeres. Across centromeres, specific types of TEs participate in genomic conflict, a balancing act wherein they are actively inserting into centromeric domains yet are harnessed for the recruitment of centromeric histones and potentially new centromere formation.
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Affiliation(s)
- Savannah J Klein
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
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Hernández-Saavedra D, Strakovsky RS, Ostrosky-Wegman P, Pan YX. Epigenetic Regulation of Centromere Chromatin Stability by Dietary and Environmental Factors. Adv Nutr 2017; 8:889-904. [PMID: 29141972 PMCID: PMC5683002 DOI: 10.3945/an.117.016402] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The centromere is a genomic locus required for the segregation of the chromosomes during cell division. This chromosomal region together with pericentromeres has been found to be susceptible to damage, and thus the perturbation of the centromere could lead to the development of aneuploidic events. Metabolic abnormalities that underlie the generation of cancer include inflammation, oxidative stress, cell cycle deregulation, and numerous others. The micronucleus assay, an early clinical marker of cancer, has been shown to provide a reliable measure of genotoxic damage that may signal cancer initiation. In the current review, we will discuss the events that lead to micronucleus formation and centromeric and pericentromeric chromatin instability, as well transcripts emanating from these regions, which were previously thought to be inactive. Studies were selected in PubMed if they reported the effects of nutritional status (macro- and micronutrients) or environmental toxicant exposure on micronucleus frequency or any other chromosomal abnormality in humans, animals, or cell models. Mounting evidence from epidemiologic, environmental, and nutritional studies provides a novel perspective on the origination of aneuploidic events. Although substantial evidence exists describing the role that nutritional status and environmental toxicants have on the generation of micronuclei and other nuclear aberrations, limited information is available to describe the importance of macro- and micronutrients on centromeric and pericentromeric chromatin stability. Moving forward, studies that specifically address the direct link between nutritional status, excess, or deficiency and the epigenetic regulation of the centromere will provide much needed insight into the nutritional and environmental regulation of this chromosomal region and the initiation of aneuploidy.
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Affiliation(s)
| | | | | | - Yuan-Xiang Pan
- Division of Nutritional Sciences,,Department of Food Science and Human Nutrition,,Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Champaign, IL; and
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14
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O'Leary VB, Maugg D, Smida J, Baumhoer D, Nathrath M, Ovsepian SV, Atkinson MJ. The long non-coding RNA PARTICLE is associated with WWOX and the absence of FRA16D breakage in osteosarcoma patients. Oncotarget 2017; 8:87431-87441. [PMID: 29152092 PMCID: PMC5675644 DOI: 10.18632/oncotarget.21086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023] Open
Abstract
Breakage of the fragile site FRA16D disrupts the WWOX (WW Domain Containing Oxidoreductase) tumor suppressor gene in osteosarcoma. However, the frequency of breakage is not sufficient to explain the rate of WWOX loss in pathogenesis. The involvement of non-coding RNA transcripts is proposed due to their accumulation at fragile sites, where they are advocated to influence specific chromosomal regions associated with malignancy. The long ncRNA PARTICLE (promoter of MAT2A antisense radiation-induced circulating long non-coding RNA) is transiently elevated in response to irradiation and influences epigenetic silencing modification within WWOX. It now emerges that elevated PARTICLE levels are significantly associated with FRA16D non-breakage in OS patients. Although not associated with overall survival, high PARTICLE levels were found to be significantly linked to metastasis free outcome. The transcription of both PARTICLE and WWOX are transiently responsive to exposure to low doses of radiation in osteosarcoma cell lines. Herein, a relationship between WWOX and PARTICLE transcription is suggested in human osteosarcoma cell lines representing alternative genetic backgrounds. PARTICLE over-expression ameliorated WWOX promoter activity in U2OS harboring FRA16D non-breakage. It can be concluded that the lncRNA PARTICLE influences the WWOX tumor suppressor and in the absence of WWOX FRA16D breakage, it is associated with OS metastasis-free survival.
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Affiliation(s)
- Valerie Bríd O'Leary
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Doris Maugg
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Department of Pediatrics and Children's Cancer Research Center, Technical University Munich, Munich, Germany
| | - Jan Smida
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Center, Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Michaela Nathrath
- Department of Pediatrics and Children's Cancer Research Center, Technical University Munich, Munich, Germany.,Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
| | - Saak Victor Ovsepian
- Institute of Biological and Medical Imaging, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Faculty for Electrical Engineering and Information Technology, Technical University Munich, Munich, Germany.,International Centre for Neurotherapeutics, Glasnevin, Dublin, Republic of Ireland
| | - Michael John Atkinson
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Radiation Biology, Technical University Munich, Munich, Germany
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15
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16
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Ferreira D, Meles S, Escudeiro A, Mendes-da-Silva A, Adega F, Chaves R. Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer. Chromosome Res 2016; 23:479-93. [PMID: 26293605 DOI: 10.1007/s10577-015-9482-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
For several decades, transcriptional inactivity was considered as one of the particular features of constitutive heterochromatin and, therefore, of its major component, satellite DNA sequences. However, more recently, succeeding evidences have demonstrated that these sequences can indeed be transcribed, yielding satellite non-coding RNAs with important roles in the organization and regulation of genomes. Since then, several studies have been conducted, trying to understand the function(s) of these sequences not only in the normal but also in cancer genomes. It is thought that the association between cancer and satncRNAs is mostly due to the influence of these transcripts in the genome instability, a hallmark of cancer. The few reports on satellite DNA transcription in cancer contexts point to its overexpression; however, this scenario may be far more complex, variable, and influenced by a number of factors and the exact role of satncRNAs in the oncogenic process remains poorly understood. The greater is the knowledge on the association of satncRNAs with cancer, the greater would be the opportunity to assist cancer treatment, either by the design of effective therapies targeting these molecules or by using them as biomarkers in cancer diagnosis, prognosis, and with predictive value.
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Affiliation(s)
- Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Susana Meles
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Ana Mendes-da-Silva
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
- Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Lisboa, Portugal.
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17
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Mei Q, Li X, Zhang K, Wu Z, Li X, Meng Y, Guo M, Luo G, Fu X, Han W. Genetic and Methylation-Induced Loss of miR-181a2/181b2 within chr9q33.3 Facilitates Tumor Growth of Cervical Cancer through the PIK3R3/Akt/FoxO Signaling Pathway. Clin Cancer Res 2016; 23:575-586. [PMID: 27503199 DOI: 10.1158/1078-0432.ccr-16-0303] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 07/21/2016] [Accepted: 07/29/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Qian Mei
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Xiang Li
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Kang Zhang
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Zhiqiang Wu
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Xiaolei Li
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Yuanguang Meng
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Guangbin Luo
- Case Comprehensive Cancer Centre, Case Western Reserve University, Cleveland, Ohio
| | - Xiaobing Fu
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China
| | - Weidong Han
- Department of Molecular Biology, Institute of Basic Medicine, School of Life Sciences, Chinese PLA General Hospital, Beijing, China.
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18
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Hinten M, Maclary E, Gayen S, Harris C, Kalantry S. Visualizing Long Noncoding RNAs on Chromatin. Methods Mol Biol 2016; 1402:147-164. [PMID: 26721489 DOI: 10.1007/978-1-4939-3378-5_12] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorescence in situ hybridization (FISH) enables the detection of specific nucleic acid sequences within single cells. For example, RNA FISH provides information on both the expression level and localization of RNA transcripts and, when combined with detection of associated proteins and chromatin modifications, can lend essential insights into long noncoding RNA (lncRNA) function. Epigenetic effects have been postulated for many lncRNAs, but shown for only a few. Advances in in situ techniques and microscopy, however, now allow for visualization of lncRNAs that are expressed at very low levels or are not very stable. FISH-based detections of RNA and DNA coupled with immunological staining of proteins/histone modifications offer the possibility to connect lncRNAs to epigenetic effects. Here, we describe an integrated set of protocols to detect, individually or in combination, specific RNAs, DNAs, proteins, and histone modifications in single cells at a high level of sensitivity using conventional fluorescence microscopy.
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Affiliation(s)
- Michael Hinten
- Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Emily Maclary
- Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Srimonta Gayen
- Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, 3710-D Med. Sci II SPC 5618, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA.
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19
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Affiliation(s)
- Victoria H. Meller
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Sonal S. Joshi
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Nikita Deshpande
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
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20
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Wiberg RAW, Halligan DL, Ness RW, Necsulea A, Kaessmann H, Keightley PD. Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome. Genome Biol Evol 2015; 7:2432-44. [PMID: 26272717 PMCID: PMC4558870 DOI: 10.1093/gbe/evv155] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2015] [Indexed: 12/27/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs has identified approximately 200 functional loci across the Eukarya, general surveys have found only modest or no evidence of long-term evolutionary conservation. Although this lack of conservation suggests that most lncRNAs are nonfunctional, the possibility remains that some represent recent evolutionary innovations. We examine recent selection pressures acting on lncRNAs in mouse populations. We compare patterns of within-species nucleotide variation at approximately 10,000 lncRNA loci in a cohort of the wild house mouse, Mus musculus castaneus, with between-species nucleotide divergence from the rat (Rattus norvegicus). Loci under selective constraint are expected to show reduced nucleotide diversity and divergence. We find limited evidence of sequence conservation compared with putatively neutrally evolving ancestral repeats (ARs). Comparisons of sequence diversity and divergence between ARs, protein-coding (PC) exons and lncRNAs, and the associated flanking regions, show weak, but significantly lower levels of sequence diversity and divergence at lncRNAs compared with ARs. lncRNAs conserved deep in the vertebrate phylogeny show lower within-species sequence diversity than lncRNAs in general. A set of 74 functionally characterized lncRNAs show levels of diversity and divergence comparable to PC exons, suggesting that these lncRNAs are under substantial selective constraints. Our results suggest that, in mouse populations, most lncRNA loci evolve at rates similar to ARs, whereas older lncRNAs tend to show signals of selection similar to PC genes.
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Affiliation(s)
- R Axel W Wiberg
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present address: Centre for Biological Diversity, School of Biology, University of St. Andrews, United Kingdom
| | - Daniel L Halligan
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Rob W Ness
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Anamaria Necsulea
- School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - Henrik Kaessmann
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
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21
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Russo A, Pacchierotti F, Cimini D, Ganem NJ, Genescà A, Natarajan AT, Pavanello S, Valle G, Degrassi F. Genomic instability: Crossing pathways at the origin of structural and numerical chromosome changes. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:563-580. [PMID: 25784636 DOI: 10.1002/em.21945] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/02/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
Genomic instability leads to a wide spectrum of genetic changes, including single nucleotide mutations, structural chromosome alterations, and numerical chromosome changes. The accepted view on how these events are generated predicts that separate cellular mechanisms and genetic events explain the occurrence of these types of genetic variation. Recently, new findings have shed light on the complexity of the mechanisms leading to structural and numerical chromosome aberrations, their intertwining pathways, and their dynamic evolution, in somatic as well as in germ cells. In this review, we present a critical analysis of these recent discoveries in this area, with the aim to contribute to a deeper knowledge of the molecular networks leading to adverse outcomes in humans following exposure to environmental factors. The review illustrates how several technological advances, including DNA sequencing methods, bioinformatics, and live-cell imaging approaches, have contributed to produce a renewed concept of the mechanisms causing genomic instability. Special attention is also given to the specific pathways causing genomic instability in mammalian germ cells. Remarkably, the same scenario emerged from some pioneering studies published in the 1980s to 1990s, when the evolution of polyploidy, the chromosomal effects of spindle poisons, the fate of micronuclei, were intuitively proposed to share mechanisms and pathways. Thus, an old working hypothesis has eventually found proper validation.
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Affiliation(s)
| | - Francesca Pacchierotti
- Laboratory of Toxicology, Unit of Radiation Biology and Human Health, ENEA CR Casaccia, Rome, Italy
| | - Daniela Cimini
- Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia
| | - Neil J Ganem
- Department of Pharmacology, Division of Hematology and Oncology, Boston University School of Medicine, Boston, Massachusetts
| | - Anna Genescà
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | - Sofia Pavanello
- Department of Cardiac, Thoracic and Vascular Sciences, Unit of Occupational Medicine, University of Padova, Italy
| | - Giorgio Valle
- Department of Biology, University of Padova, Padova, Italy
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22
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Vieira-da-Silva A, Louzada S, Adega F, Chaves R. A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions. Cytogenet Genome Res 2015; 145:59-67. [PMID: 25999143 DOI: 10.1159/000381840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 11/19/2022] Open
Abstract
Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes.
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Affiliation(s)
- Ana Vieira-da-Silva
- Center of Agricultural and Genomics Biotechnology (CGBA), University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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23
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Feliciello I, Akrap I, Brajković J, Zlatar I, Ugarković Đ. Satellite DNA as a driver of population divergence in the red flour beetle Tribolium castaneum. Genome Biol Evol 2014; 7:228-39. [PMID: 25527837 PMCID: PMC4316633 DOI: 10.1093/gbe/evu280] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tandemly repeated satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected. Here, we characterize minor TCAST2 satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 satellite DNA which differ in monomer size, genome organization, and subfamily specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin whereas Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific satellite DNA profiles. Partial organization of TCAST2 satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level.
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Affiliation(s)
- Isidoro Feliciello
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia Laboratory of Experimental Biology, Department of Clinical Medicine and Surgery, University of Naples Federico II, Italy
| | - Ivana Akrap
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Josip Brajković
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivo Zlatar
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Đurđica Ugarković
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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24
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Chowdhury D, Choi YE, Brault ME. Charity begins at home: non-coding RNA functions in DNA repair. Nat Rev Mol Cell Biol 2013; 14:181-9. [PMID: 23385724 DOI: 10.1038/nrm3523] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the past decade, evolutionarily conserved microRNAs (miRNAs) have been characterized as regulators of almost every cellular process and signalling pathway. There is now emerging evidence that this new class of regulators also impinges on the DNA damage response (DDR). Both miRNAs and other small non-coding RNAs (ncRNAs) are induced at DNA breaks and mediate the repair process. These intriguing observations raise the possibility that crosstalk between ncRNAs and the DDR might provide a means of efficient and accurate DNA repair and facilitate the maintenance of genomic stability.
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Affiliation(s)
- Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.
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25
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Lindsay J, Carone DM, Brown J, Hall L, Qureshi S, Mitchell SE, Jannetty N, Hannon G, Renfree M, Pask A, O'Neill M, O'Neill R. Unique small RNA signatures uncovered in the tammar wallaby genome. BMC Genomics 2012; 13:559. [PMID: 23075437 PMCID: PMC3576234 DOI: 10.1186/1471-2164-13-559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 10/08/2012] [Indexed: 12/12/2022] Open
Abstract
Background Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs). Results Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar. We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. An additional nine genes were identified in tammar that do not have an orthologous miRNA target in human and likely represent novel miRNA-regulated genes in the tammar. A survey of the tammar gonadal piRNAs shows that these small RNAs are enriched in retroelements and carry members from both marsupial and tammar-specific repeat classes. Lastly, this study includes the first in-depth analyses of the newly discovered crasiRNAs. These small RNAs are derived largely from centromere-enriched retroelements, including a novel SINE. Conclusions This study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein. The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function.
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Affiliation(s)
- James Lindsay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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26
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Molecular cytogenetics: karyotype evolution, phylogenomics and future prospects. Heredity (Edinb) 2012; 108:1-3. [PMID: 22167088 DOI: 10.1038/hdy.2011.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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