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Koivuluoma S, Vorimo S, Mattila TM, Tervasmäki A, Kumpula T, Kuismin O, Winqvist R, Moilanen J, Mantere T, Pylkäs K. Truncating TINF2 p.Tyr312Ter variant and inherited breast cancer susceptibility. Fam Cancer 2023; 22:13-17. [PMID: 35590014 PMCID: PMC9829577 DOI: 10.1007/s10689-022-00295-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/08/2022] [Indexed: 01/13/2023]
Abstract
TINF2 is a critical subunit of the shelterin complex, which protects and maintains the length of telomeres. Pathogenic missense and truncating TINF2 mutations are causative for dyskeratosis congenita (DC), a rare, dominantly inherited bone marrow failure syndrome characterized by mucocutaneous abnormalities and cancer predisposition. Recent reports indicate that specific TINF2 truncating mutations act as high penetrance cancer predisposition alleles outside DC context, including breast cancer in their tumor spectrum. Here, we have evaluated the role of germline mutations in TINF2 and other shelterin genes in inherited breast cancer susceptibility using exome sequencing data from 98 Northern Finnish breast cancer cases with indication of inherited disease predisposition as a discovery cohort. A single protein truncating variant, TINF2 p.Tyr312Ter, was identified in one of the cases (1/98), and four more carriers were observed in the subsequently genotyped unselected breast cancer cohort (4/1904). None of the carriers were reported to have DC. TINF2 p.Tyr312Ter resulted in stable short form of mRNA transcript, and normal telomere length has been indicated by a recent report. Although recurrent in cases (total of 5/2095), TINF2 p.Tyr312Ter is also present in Finnish population controls (8/12,517), and the observed 4-fold higher frequency in cases falls at most into the range of moderate breast cancer risk alleles (OR 3.74, 95% CI 1.22-11.45, p = 0.029). Current results indicate that not all TINF2 truncating variants are high cancer risk alleles and add further evidence that different TINF2 mutations can have very diverse effects on the disease phenotype.
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Affiliation(s)
- Susanna Koivuluoma
- grid.10858.340000 0001 0941 4873Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220 Aapistie 5A, Oulu, Finland
| | - Sandra Vorimo
- grid.10858.340000 0001 0941 4873Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220 Aapistie 5A, Oulu, Finland
| | - Tiina M. Mattila
- grid.10858.340000 0001 0941 4873Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220 Aapistie 5A, Oulu, Finland
| | - Anna Tervasmäki
- grid.10858.340000 0001 0941 4873Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220 Aapistie 5A, Oulu, Finland
| | - Timo Kumpula
- grid.10858.340000 0001 0941 4873Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220 Aapistie 5A, Oulu, Finland
| | - Outi Kuismin
- grid.10858.340000 0001 0941 4873Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Robert Winqvist
- grid.10858.340000 0001 0941 4873Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220 Aapistie 5A, Oulu, Finland
| | - Jukka Moilanen
- grid.10858.340000 0001 0941 4873Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Tuomo Mantere
- grid.10858.340000 0001 0941 4873Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220 Aapistie 5A, Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, NordLab Oulu, University of Oulu, 90220, Aapistie 5A, Oulu, Finland.
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Antonov I, Marakhonov A, Zamkova M, Medvedeva Y. ASSA: Fast identification of statistically significant interactions between long RNAs. J Bioinform Comput Biol 2018; 16:1840001. [PMID: 29375012 DOI: 10.1142/s0219720018400012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The discovery of thousands of long noncoding RNAs (lncRNAs) in mammals raises a question about their functionality. It has been shown that some of them are involved in post-transcriptional regulation of other RNAs and form inter-molecular duplexes with their targets. Sequence alignment tools have been used for transcriptome-wide prediction of RNA-RNA interactions. However, such approaches have poor prediction accuracy since they ignore RNA's secondary structure. Application of the thermodynamics-based algorithms to long transcripts is not computationally feasible on a large scale. Here, we describe a new computational pipeline ASSA that combines sequence alignment and thermodynamics-based tools for efficient prediction of RNA-RNA interactions between long transcripts. To measure the hybridization strength, the sum energy of all the putative duplexes is computed. The main novelty implemented in ASSA is the ability to quickly estimate the statistical significance of the observed interaction energies. Most of the functional hybridizations between long RNAs were classified as statistically significant. ASSA outperformed 11 other tools in terms of the Area Under the Curve on two out of four test sets. Additionally, our results emphasized a unique property of the [Formula: see text] repeats with respect to the RNA-RNA interactions in the human transcriptome. ASSA is available at https://sourceforge.net/projects/assa/.
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Affiliation(s)
- Ivan Antonov
- * Institute of Bioengineering, Federal Research Center Fundamentals of Biotechnology RAS, Moscow 117312, Russia.,† Department of Molecular and Biological Physics & Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Andrey Marakhonov
- ‡ Laboratory of Functional Analysis of the Genome, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.,§ Federal State Scientific Budgetary Institution, Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Maria Zamkova
- ¶ Russian N.N. Blokhin Cancer Research Center, Moscow 115478, Russia
| | - Yulia Medvedeva
- * Institute of Bioengineering, Federal Research Center Fundamentals of Biotechnology RAS, Moscow 117312, Russia.,† Department of Molecular and Biological Physics & Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.,∥ Vavilov Institute of General Genetics, RAS, Moscow 119333, Russia
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Chen H, Du G, Song X, Li L. Non-coding Transcripts from Enhancers: New Insights into Enhancer Activity and Gene Expression Regulation. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:201-207. [PMID: 28599852 PMCID: PMC5487526 DOI: 10.1016/j.gpb.2017.02.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 02/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological processes. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs (eRNAs). The eRNAs are not merely the by-product of the enhancer transcription. In fact, many of them directly exert or regulate enhancer activity in gene activation through diverse mechanisms. Here, we provide an overview of enhancer activity, transcription of enhancer itself, characteristics of eRNAs, as well as their roles in regulating enhancer activity and gene expression.
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Affiliation(s)
- Hongjun Chen
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Guangshi Du
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Ling Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.
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Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection. Sci Rep 2016; 6:32348. [PMID: 27586304 PMCID: PMC5009348 DOI: 10.1038/srep32348] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 08/01/2016] [Indexed: 02/07/2023] Open
Abstract
Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target sites within exonized Alus, and analyzed conservation of these targets across primates. We observed that two miRNAs (miR-15a-3p and miR-302d-3p) elevated in stress response, target RAD1, GTSE1, NR2C1, FKBP9 and UBE2I exclusively within Alu. These genes map onto the p53 regulatory network. Ectopic overexpression of miR-15a-3p downregulates GTSE1 and RAD1 at the protein level and enhances cell survival. This Alu-mediated fine-tuning seems to be unique to humans as evident from the absence of orthologous sites in other primate lineages. We further analyzed signatures of selection on Alu-miRNA targets in the genome, using 1000 Genomes Phase-I data. We found that 198 out of 3177 Alu-exonized genes exhibit signatures of selection within Alu-miRNA sites, with 60 of them containing SNPs supported by multiple evidences (global-FST > 0.3, pair-wise-FST > 0.5, Fay-Wu’s H < −20, iHS > 2.0, high ΔDAF) and implicated in p53 network. We propose that by affecting multiple genes, Alu-miRNA interactions have the potential to facilitate population-level adaptations in response to environmental challenges.
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Li Y, Huang C, Feng P, Jiang Y, Wang W, Zhou D, Chen L. Aberrant expression of miR-153 is associated with overexpression of hypoxia-inducible factor-1α in refractory epilepsy. Sci Rep 2016; 6:32091. [PMID: 27554040 PMCID: PMC4995460 DOI: 10.1038/srep32091] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/02/2016] [Indexed: 02/06/2023] Open
Abstract
Evidence suggest that overexpression of hypoxia-inducible factor-1α (HIF-1α) is linked to multidrug resistance of epilepsy. Here we explored whether aberrant expression of HIF-1α is regulated by miRNAs. Genome-wide microRNA expression profiling was performed on temporal cortex resected from mesial temporal lobe epilepsy (mTLE) patients and age-matched controls. miRNAs that are putative regulator of HIF-1α were predicted via target scan and confirmed by real-time quantitative polymerase chain reaction (RT-qPCR). Mimics or miRNA morpholino inhibitors were transfected in astrocytes and luciferase reporter assay was applied to detect HIF-11α expression. Microarray profiling identified down-regulated miR-153 as a putative regulator of HIF-1α in temporal cortex resected from surgical mTLE patients. RT-qPCR confirmed down-regulation of miR-153 in plasma of mTLE patients in an independent validation cohort. Knockdown of miR-153 significantly enhanced expression of HIF-1α while forced expression of miR-153 dramatically inhibited HIF-1α expression in pharmacoresistant astrocyte model. Luciferase assay established that miR-153 might inhibit HIF-1α expression via directly targeting two binding sites in the 3′UTR region of HIF-1α transcript. These data suggest that down-regulation of miR-153 may contribute to enhanced expression of HIF-1α in mTLE and serve as a novel biomarker and treatment target for epilepsy.
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Affiliation(s)
- Yaohua Li
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Cheng Huang
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Peimin Feng
- Department of integrated traditional and western medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, People's Republic of China
| | - Yanping Jiang
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Wei Wang
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Dong Zhou
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Lei Chen
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
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Kurokawa R. Long noncoding RNA as a regulator for transcription. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2016; 51:29-41. [PMID: 21287132 DOI: 10.1007/978-3-642-16502-3_2] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Investigation of noncoding RNAs is in rapid progress, especially regarding translational repression by small (short) noncoding RNAs like microRNAs with 20-25 nucleotide-lengths, while long noncoding RNAs with nucleotide length of more than two hundred are also emerging. Indeed, our analysis has revealed that a long noncoding RNA transcribed from cyclin D1 promoter of 200 and 300 nucleotides exerts transcriptional repression through its binding protein TLS instead of translational repression. Translational repression is executed by short noncoding RNAs, while transcriptional repression is mainly done by long noncoding RNAs. These long noncoding RNAs are heterogeneous molecules and employ divergent molecular mechanisms to exert transcriptional repression. In this review, I overview recent publications regarding the transcription regulation by long noncoding RNAs and explore their biological significance. In addition, the relation between a random transcriptional activity of RNA polymerase II and the origin of long noncoding RNAs is discussed.
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Affiliation(s)
- Riki Kurokawa
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Hidaka-shi, Saitama-Ken, 350-1241, Japan,
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Deng W, Babu IR, Su D, Yin S, Begley TJ, Dedon PC. Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation. PLoS Genet 2015; 11:e1005706. [PMID: 26670883 PMCID: PMC4689569 DOI: 10.1371/journal.pgen.1005706] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/06/2015] [Indexed: 12/30/2022] Open
Abstract
Post-transcriptional modifications of transfer RNAs (tRNAs) have long been recognized to play crucial roles in regulating the rate and fidelity of translation. However, the extent to which they determine global protein production remains poorly understood. Here we use quantitative proteomics to show a direct link between wobble uridine 5-methoxycarbonylmethyl (mcm5) and 5-methoxy-carbonyl-methyl-2-thio (mcm5s2) modifications catalyzed by tRNA methyltransferase 9 (Trm9) in tRNAArg(UCU) and tRNAGlu(UUC) and selective translation of proteins from genes enriched with their cognate codons. Controlling for bias in protein expression and alternations in mRNA expression, we find that loss of Trm9 selectively impairs expression of proteins from genes enriched with AGA and GAA codons under both normal and stress conditions. Moreover, we show that AGA and GAA codons occur with high frequency in clusters along the transcripts, which may play a role in modulating translation. Consistent with these results, proteins subject to enhanced ribosome pausing in yeast lacking mcm5U and mcm5s2U are more likely to be down-regulated and contain a larger number of AGA/GAA clusters. Together, these results suggest that Trm9-catalyzed tRNA modifications play a significant role in regulating protein expression within the cell. Here we present evidence for a more complicated role for transfer RNAs (tRNAs) than as mere adapters that link the genetic code in messenger RNA (mRNA) to the amino acid sequence of a protein during translation. tRNAs have long been known to be modified with dozens of different chemical structures other than the 4 canonical ribonucleosides, though the role of these modifications in controlling translation is poorly understood. By quantifying the expression of thousands of proteins in the yeast S. cerevisiae, we identified a mechanistic link between modified ribonucleosides located at the wobble position of two tRNAs, tRNAArg(UCU) and tRNAGlu(UUC), and the translation of proteins derived from genes enriched with codons read by these tRNAs: AGA and GAA. In cells lacking the enzyme that inserts these modifications, tRNA methyltransferase 9 (Trm9), we found a significant reduction in proteins from genes enriched with AGA and GAA codons and with runs of these codons. Also, mRNAs enriched with runs of AGA and GAA codons are subject to stalled translation on ribosomes in yeast lacking mcm5U and mcm5s2U. Together, these results reveal a distinct role for Trm9-catalyzed tRNA modifications in selectively regulating the expression of proteins enriched with AGA and GAA codons.
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Affiliation(s)
- Wenjun Deng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - I. Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dan Su
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas J. Begley
- SUNY College of Nanoscale Science and Engineering, Albany, New York, United States of America
- RNA Institute and Cancer Research Center, University at Albany, State University of New York, Albany, New York, United States of America
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Singapore-MIT Alliance for Research and Technology, Singapore
- * E-mail:
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Chen S, Shao C, Xu M, Ji J, Xie Y, Lei Y, Wang X. Macrophage infiltration promotes invasiveness of breast cancer cells via activating long non-coding RNA UCA1. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:9052-9061. [PMID: 26464647 PMCID: PMC4583879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/21/2015] [Indexed: 06/05/2023]
Abstract
There is now considerable evidence supporting the view that macrophage infiltration is playing a critical role in the proliferation and progression of breast cancer but the underlying molecular mechanisms remain largely unknown. To this end, using long non-coding RNA (lncRNA) expression profiling, we examined changes in lncRNA expression in breast cancer cells treated with conditioned medium (CM) from cultured human THP-1 macrophages. We found that treatment with macrophage CM induced the expression of numerous lncRNAs, including urothelial cancer associated 1 (UCA1). Knockdown of UCA1 using shRNA inhibited AKT phosphorylation and abolished invasiveness of tumor cells induced by macrophage CM. Consistent with these results; we further showed that UCA1 level was significantly enhanced in human primary breast tumors and correlated with advanced clinical stage, supporting its role in promoting carcinogenesis and progression of breast cancer. Together, these results suggest that macrophage could promote invasiveness of breast cancer cells by enhancing expression of lncRNA UCA1.
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Affiliation(s)
- Shuzheng Chen
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Chuxiao Shao
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Min Xu
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Jiansong Ji
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Yanru Xie
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Yongliang Lei
- Lishui Center for Disease Control and PreventionLishui, Zhejiang, China
| | - Xiaoguang Wang
- Lishui Center for Disease Control and PreventionLishui, Zhejiang, China
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Wang H, Cui K, Xu K, Xu S. Association between plasma homocysteine and progression of early nephropathy in type 2 diabetic patients. Int J Clin Exp Med 2015; 8:11174-11180. [PMID: 26379920 PMCID: PMC4565303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/24/2015] [Indexed: 06/05/2023]
Abstract
There is now growing evidence supporting the association between renal insufficiency and accumulation of plasma homocysteine (Hcy). However, the role of Hcy in the development of diabetic nephropathy (DN) in type 2 diabetic patients is not clearly elucidated. To this end, we performed a prospective observational study in 208 patients and 49 controls. We show that baseline level of Hcy is significantly enhanced in patients with DN and is associated with the severity of the disease. Focusing on patients at early DN stage (n = 157), after four-year follow-up, we find that increase in plasma Hcy level correlates with greater renal failure characterized by faster decline in estimated glomerular filtration rate (eGFR). Using a multivariate linear regression model, we show that plasma Hcy remains significantly associated with eGFR decline after controlling for other progression promoters. Our results support that plasma Hcy is an independent risk factor as well as an early predictor for DN progression in type 2 diabetic patients.
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Affiliation(s)
- Huan Wang
- Department of Nephrology, Xinxiang Central HospitalHenan, China
| | - Kai Cui
- Department of General Tumor Surgery, Xinxiang Central HospitalHenan, China
| | - Ke Xu
- Department of Nephrology, Xinxiang Central HospitalHenan, China
| | - Shixin Xu
- Department of Nephrology, Xinxiang Central HospitalHenan, China
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Chen SS, Song J, Tu XY, Zhao JH, Ye XQ. The association between MMP-12 82 A/G polymorphism and susceptibility to various malignant tumors: a meta-analysis. Int J Clin Exp Med 2015; 8:10845-10854. [PMID: 26379878 PMCID: PMC4565261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/09/2015] [Indexed: 06/05/2023]
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases responsible for degrading essentially all components of the extracellular matrix (ECM). Accumulating evidence suggests that MMPs might play a critical role in growth, invasion, and metastasis of malignant tumors. A single nucleotide polymorphism (SNP) in the promoter region of MMP-12, MMP-12 82 A/G (rs2276109), has been recognized to play a critical role in regulating the expression of MMP-12, however, its correlation with tumor susceptibility remains controversial. To address this issue, we performed meta-analysis to investigate the association MMP-12 82 A/G polymorphism and susceptibility of nine malignant tumors from 11 studies, including 6153 cancer patients and 6838 controls. Two reviewers independently screened studies for eligibility and extracted data for included studies. While overall no evident association between MMP-12 82 A/G and tumor susceptibility was observed, subgroup analysis revealed a specific role of G allele in increasing the susceptibility for epithelial ovarian carcinoma (EOC) using the allele model (fixed effects OR = 2.45, 95% CI = 1.46-4.10, P = 0.001) and the dominant model (fixed effects OR = 2.52, 95% CI = 1.49-4.24, P = 0.001). We thus suggest that G allele of MMP-12 82 A/G polymorphism is a genetic risk factor for EOC.
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Affiliation(s)
- Sheng-Song Chen
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University Nanchang 330006, China
| | - Juan Song
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University Nanchang 330006, China
| | - Xiao-Yun Tu
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University Nanchang 330006, China
| | - Ji-Hua Zhao
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University Nanchang 330006, China
| | - Xiao-Qun Ye
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University Nanchang 330006, China
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Zhou Y, Wu K, Jiang J, Huang J, Zhang P, Zhu Y, Hu G, Lang J, Shi Y, Hu L, Huang T, Kong X. Integrative analysis reveals enhanced regulatory effects of human long intergenic non-coding RNAs in lung adenocarcinoma. J Genet Genomics 2015; 42:423-36. [PMID: 26336799 DOI: 10.1016/j.jgg.2015.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/29/2015] [Accepted: 07/02/2015] [Indexed: 12/24/2022]
Abstract
Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs (lincRNAs) play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed "regulatory lincRNAs", representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GAS5, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.
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Affiliation(s)
- You Zhou
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Kai Wu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Jianping Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinfei Huang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Peiwei Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Yufei Zhu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Guohong Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Jingyu Lang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Yufang Shi
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Landian Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Tao Huang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China.
| | - Xiangyin Kong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China.
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Sun FF, Hu YH, Xiong LP, Tu XY, Zhao JH, Chen SS, Song J, Ye XQ. Enhanced expression of stem cell markers and drug resistance in sphere-forming non-small cell lung cancer cells. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:6287-6300. [PMID: 26261505 PMCID: PMC4525839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/17/2015] [Indexed: 06/04/2023]
Abstract
There is growing evidence suggesting that cancer stem cells (CSCs) are playing critical roles in tumor progression, metastasis and drug resistance. However, the role of CSCs in non-small cell lung cancer (NSCLC) remains elusive. In this study, we enriched for stem-like cells from tumor spheres derived from NSCLC cell line A549 cultured in serum-free medium. Our results showed that sphere-derived cells expressed various stem cell markers such as CD44, CD133, Sox2 and Oct4. Compared with the corresponding cells in monolayer cultures, sphere-derived cells showed marked morphologic changes and increased expression of the stem cell markers CD133. Furthermore, we found that sphere-derived cells exhibited increased proliferation, cell-cycle progression as well as drug-resistant properties as compared to A549 adherent cells. Consistently, expression of several drug resistance proteins, including lung resistance-related protein (LRP), glutathion-S-transferase-π (GST-π) and multidrug resistance proteins-1 (MRP1) were all significantly enhanced in sphere-derived cells. These results indicate the enrichment of CSCs in sphere cultures and support their role in regulating drug resistance in NSCLC.
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Affiliation(s)
- Feng-Feng Sun
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang UniversityNanchang 330006, China
| | - Yong-He Hu
- The General Hospital of Chengdu Military RegionChengdu 610083, Sichuan Province, China
| | - Lv-Ping Xiong
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang UniversityNanchang 330006, China
| | - Xiao-Yun Tu
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang UniversityNanchang 330006, China
| | - Ji-Hua Zhao
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang UniversityNanchang 330006, China
| | - Sheng-Song Chen
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang UniversityNanchang 330006, China
| | - Juan Song
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang UniversityNanchang 330006, China
| | - Xiao-Qun Ye
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang UniversityNanchang 330006, China
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Qiu F, Xiong JP, Deng J, Xiang XJ. TRIM29 functions as an oncogene in gastric cancer and is regulated by miR-185. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:5053-5061. [PMID: 26191199 PMCID: PMC4503071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/15/2015] [Indexed: 06/04/2023]
Abstract
Tripartite motif-containing 29 (TRIM29) belongs to TRIM family of transcription factors and may function as an oncogene or a tumor suppressor depending on the tumor types. Overexpression of TRIM29 is frequently observed in gastric cancer but the underlying mechanisms remain largely unknown. In the present study, we investigated the function of TRIM29 in gastric cancer-derived cell line MGC803. RNAi-mediated silencing of TRIM29 resulted in significantly reduced cell proliferation and colony formation, as well as G1-S cell cycle arrest and apoptosis. Interestingly, expression levels of β-catenin, cyclin D1 and c-Myc were all downregulated in TRIM29 knockdown cells, indicating that TRIM29 is involved in regulating the activity of Wnt/β-catenin signaling pathway. Furthermore, based on target prediction and luciferase assay, we identified TRIM29 as a potential target of miR-185, which is frequently downregulated in gastric cancer. Over-expression of miR-185 in MGC803 cells inhibited TRIM29 expression and activity of Wnt/β-catenin signaling. Taken together, our results suggest that TRIM29 functions as an oncogene in gastric cancer and is regulated by miR-185.
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Affiliation(s)
- Feng Qiu
- Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, People’s Republic of China
- Department of Oncology, the First Affiliated Hospital of Nanchang UniversityNanchang 330006, People’s Republic of China
| | - Jian-Ping Xiong
- Department of Oncology, the First Affiliated Hospital of Nanchang UniversityNanchang 330006, People’s Republic of China
| | - Jun Deng
- Department of Oncology, the First Affiliated Hospital of Nanchang UniversityNanchang 330006, People’s Republic of China
| | - Xiao-Jun Xiang
- Department of Oncology, the First Affiliated Hospital of Nanchang UniversityNanchang 330006, People’s Republic of China
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Regulatory Roles for Long ncRNA and mRNA. Cancers (Basel) 2013; 5:462-90. [PMID: 24216986 PMCID: PMC3730338 DOI: 10.3390/cancers5020462] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/05/2013] [Accepted: 04/19/2013] [Indexed: 01/31/2023] Open
Abstract
Recent advances in high-throughput sequencing technology have identified the transcription of a much larger portion of the genome than previously anticipated. Especially in the context of cancer it has become clear that aberrant transcription of both protein-coding and long non-coding RNAs (lncRNAs) are frequent events. The current dogma of RNA function describes mRNA to be responsible for the synthesis of proteins, whereas non-coding RNA can have regulatory or epigenetic functions. However, this distinction between protein coding and regulatory ability of transcripts may not be that strict. Here, we review the increasing body of evidence for the existence of multifunctional RNAs that have both protein-coding and trans-regulatory roles. Moreover, we demonstrate that coding transcripts bind to components of the Polycomb Repressor Complex 2 (PRC2) with similar affinities as non-coding transcripts, revealing potential epigenetic regulation by mRNAs. We hypothesize that studies on the regulatory ability of disease-associated mRNAs will form an important new field of research.
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Pandey R, Mandal AK, Jha V, Mukerji M. Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism. Genome Biol 2011; 12:R117. [PMID: 22112862 PMCID: PMC3334603 DOI: 10.1186/gb-2011-12-11-r117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/09/2011] [Accepted: 11/23/2011] [Indexed: 01/22/2023] Open
Abstract
Background Alu RNAs are present at elevated levels in stress conditions and, consequently, Alu repeats are increasingly being associated with the physiological stress response. Alu repeats are known to harbor transcription factor binding sites that modulate RNA pol II transcription and Alu RNAs act as transcriptional co-repressors through pol II binding in the promoter regions of heat shock responsive genes. An observation of a putative heat shock factor (HSF) binding site in Alu led us to explore whether, through HSF binding, these elements could further contribute to the heat shock response repertoire. Results Alu density was significantly enriched in transcripts that are down-regulated following heat shock recovery in HeLa cells. ChIP analysis confirmed HSF binding to a consensus motif exhibiting positional conservation across various Alu subfamilies, and reporter constructs demonstrated a sequence-specific two-fold induction of these sites in response to heat shock. These motifs were over-represented in the genic regions of down-regulated transcripts in antisense oriented Alus. Affymetrix Exon arrays detected antisense signals in a significant fraction of the down-regulated transcripts, 50% of which harbored HSF sites within 5 kb. siRNA knockdown of the selected antisense transcripts led to the over-expression, following heat shock, of their corresponding down-regulated transcripts. The antisense transcripts were significantly enriched in processes related to RNA pol III transcription and the TFIIIC complex. Conclusions We demonstrate a non-random presence of Alu repeats harboring HSF sites in heat shock responsive transcripts. This presence underlies an antisense-mediated mechanism that represents a novel component of Alu and HSF involvement in the heat shock response.
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Affiliation(s)
- Rajesh Pandey
- Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR-IGIB), Delhi- India
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Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res 2011; 21:1916-28. [PMID: 21994248 DOI: 10.1101/gr.108753.110] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes--especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ∼2% of their synonymous sites. We collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape.
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Affiliation(s)
- Michael F Lin
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Pandey R, Mukerji M. From 'JUNK' to Just Unexplored Noncoding Knowledge: the case of transcribed Alus. Brief Funct Genomics 2011; 10:294-311. [DOI: 10.1093/bfgp/elr029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Wang X, Song X, Glass CK, Rosenfeld MG. The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs. Cold Spring Harb Perspect Biol 2011; 3:a003756. [PMID: 20573714 DOI: 10.1101/cshperspect.a003756] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A major surprise arising from genome-wide analyses has been the observation that the majority of the genome is transcribed, generating noncoding RNAs (ncRNAs). It is still an open question whether some or all of these ncRNAs constitute functional networks regulating gene transcriptional programs. However, in light of recent discoveries and given the diversity and flexibility of long ncRNAs and their abilities to nucleate molecular complexes and to form spatially compact arrays of complexes, it becomes likely that many or most ncRNAs act as sensors and integrators of a wide variety of regulated transcriptional responses and probably epigenetic events. Because many RNA-binding proteins, on binding RNAs, show distinct allosteric conformational alterations, we suggest that a ncRNA/RNA-binding protein-based strategy, perhaps in concert with several other mechanistic strategies, serves to integrate transcriptional, as well as RNA processing, regulatory programs.
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Affiliation(s)
- Xiangting Wang
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093-0651, USA
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Kurokawa R. Promoter-associated long noncoding RNAs repress transcription through a RNA binding protein TLS. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 722:196-208. [PMID: 21915790 DOI: 10.1007/978-1-4614-0332-6_12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The majority of the human genome is found to be transcribed and generates mostly noncoding (nc) RNAs that do not possess protein information. MicroRNAs are one of the well-identified small ncRNAs, but occupy merely a fraction of ncRNAs. Long (large) ncRNAs are emerging as a novel class of ncRNAs, but knowledge of these ncRNAs is far less accumulated. Long ncRNAs are tentatively classified as an ncRNA species containing more than 200 nucleotides. Recently, a long promoter-associated ncRNA (pncRNA) has been identified to be transcribed from the cyclin D1 promoter upon induction by genotoxic factors like ionizing-irradiation. The cyclin D1 pncRNA is specifically bound with an RNA-binding protein TLS (Translocated in liposarcoma) and exerts transcriptional repression through histone acetyltransferase (HAT) inhibitory activity. Analysis of TLS and the pncRNAs could provide a model for elucidating their roles inregulation of mammalian transcriptional programs. The pncRNA binding to TLS turns out to be an essential event for the HAT inhibitory activity. A key consensus sequence of the pncRNA is composed of GGUG, while not every RNA sequence bearing GGUG is targeted by TLS, suggesting that a secondary structure of the GGUG-bearing RNAs is also involved in recognition by TLS. Taken together, TLS is a unique mediator between signals of the long ncRNAs and transcription, suggesting that RNA networking functions in living cells.(1-3).
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Affiliation(s)
- Riki Kurokawa
- Saitama Medical University, Yamane, Hidaka-shi, Saitama-Ken, Japan.
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Saxena A, Carninci P. Whole transcriptome analysis: what are we still missing? WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:527-43. [PMID: 21197667 DOI: 10.1002/wsbm.135] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New technologies such as tag-based sequencing and tiling arrays have provided unique insights into the transcriptional output of cells. Many new RNA classes have been uncovered in the past decade, despite limitations in current technologies. Even as the repertoire of known functional elements of the transcriptome increases and contemporary technologies become mainstream, inadequacies in conventional protocols for library preparation, sequencing and mapping continue to hamper revelation of the entire transcriptome of cells. In this article, we review current protocols and outline their deficiencies. We also provide our view on what we may be overlooking in the transcriptome, despite exhaustive investigations, and indicate future areas of technological development and research.
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Affiliation(s)
- Alka Saxena
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi, Japan
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