1
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Vaasjo LO. LncRNAs and Chromatin Modifications Pattern m6A Methylation at the Untranslated Regions of mRNAs. Front Genet 2022; 13:866772. [PMID: 35368653 PMCID: PMC8968631 DOI: 10.3389/fgene.2022.866772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/16/2022] Open
Abstract
New roles for RNA in mediating gene expression are being discovered at an alarming rate. A broad array of pathways control patterning of N6-methyladenosine (m6A) methylation on RNA transcripts. This review comprehensively discusses long non-coding RNAs (lncRNAs) as an additional dynamic regulator of m6A methylation, with a focus on the untranslated regions (UTRs) of mRNAs. Although there is extensive literature describing m6A modification of lncRNA, the function of lncRNA in guiding m6A writers has not been thoroughly explored. The independent control of lncRNA expression, its heterogeneous roles in RNA metabolism, and its interactions with epigenetic machinery, alludes to their potential in dynamic patterning of m6A methylation. While epigenetic regulation by histone modification of H3K36me3 has been demonstrated to pattern RNA m6A methylation, these modifications were specific to the coding and 3′UTR regions. However, there are observations that 5′UTR m6A is distinct from that of the coding and 3′UTR regions, and substantial evidence supports the active regulation of 5′UTR m6A methylation. Consequently, two potential mechanisms in patterning the UTRs m6A methylation are discussed; (1) Anti-sense lncRNA (AS-lncRNA) can either bind directly to the UTR, or (2) act indirectly via recruitment of chromatin-modifying complexes to pattern m6A. Both pathways can guide the m6A writer complex, facilitate m6A methylation and modulate protein translation. Findings in the lncRNA-histone-m6A axis could potentially contribute to the discovery of new functions of lncRNAs and clarify lncRNA-m6A findings in translational medicine.
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Affiliation(s)
- Lee O. Vaasjo
- Cellular and Molecular Biology, Tulane University, New Orleans, LA, United States
- Neuroscience Program, Brain Institute, Tulane University, New Orleans, LA, United States
- *Correspondence: Lee O. Vaasjo,
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2
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Abrahamsson S, Eiengård F, Rohlin A, Dávila López M. PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data. BMC Bioinformatics 2022; 23:59. [PMID: 35114952 PMCID: PMC8812246 DOI: 10.1186/s12859-022-04583-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Processed pseudogenes (PΨgs) are disabled gene copies that are transcribed and may affect expression of paralogous genes. Moreover, their insertion in the genome can disrupt the structure or the regulatory region of a gene, affecting its expression level. These events have been identified as occurring mutations during cancer development, thus being able to identify PΨgs and their location will improve their impact on diagnostic testing, not only in cancer but also in inherited disorders. RESULTS We have implemented PΨFinder (P-psy-finder), a tool that identifies PΨgs, annotates known ones and predicts their insertion site(s) in the genome. The tool screens alignment files and provides user-friendly summary reports and visualizations. To demonstrate its applicability, we scanned 218 DNA samples from patients screened for hereditary colorectal cancer. We detected 423 PΨgs distributed in 96% of the samples, comprising 7 different parent genes. Among these, we confirmed the well-known insertion site of the SMAD4-PΨg within the last intron of the SCAI gene in one sample. While for the ubiquitous CBX3-PΨg, present in 82.6% of the samples, we found it reversed inserted in the second intron of the C15ORF57 gene. CONCLUSIONS PΨFinder is a tool that can automatically identify novel PΨgs from DNA sequencing data and determine their location in the genome with high sensitivity (95.92%). It generates high quality figures and tables that facilitate the interpretation of the results and can guide the experimental validation. PΨFinder is a complementary analysis to any mutational screening in the identification of disease-causing mutations within cancer and other diseases.
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Affiliation(s)
- Sanna Abrahamsson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 115, 405 30, Gothenburg, Sweden
| | - Frida Eiengård
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Rohlin
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Unit of Genetic Analysis and Bioinformatics, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Marcela Dávila López
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 115, 405 30, Gothenburg, Sweden.
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3
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Metastatic EMT Phenotype Is Governed by MicroRNA-200-Mediated Competing Endogenous RNA Networks. Cells 2021; 11:cells11010073. [PMID: 35011635 PMCID: PMC8749983 DOI: 10.3390/cells11010073] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is a fundamental physiologically relevant process that occurs during morphogenesis and organ development. In a pathological setting, the transition from epithelial toward mesenchymal cell phenotype is hijacked by cancer cells, allowing uncontrolled metastatic dissemination. The competing endogenous RNA (ceRNA) hypothesis proposes a competitive environment resembling a large-scale regulatory network of gene expression circuits where alterations in the expression of both protein-coding and non-coding genes can make relevant contributions to EMT progression in cancer. The complex regulatory diversity is exerted through an array of diverse epigenetic factors, reaching beyond the transcriptional control that was previously thought to single-handedly govern metastatic dissemination. The present review aims to unravel the competitive relationships between naturally occurring ceRNA transcripts for the shared pool of the miRNA-200 family, which play a pivotal role in EMT related to cancer dissemination. Upon acquiring more knowledge and clinical evidence on non-genetic factors affecting neoplasia, modulation of the expression levels of diverse ceRNAs may allow for the development of novel prognostic/diagnostic markers and reveal potential targets for the disruption of cancer-related EMT.
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4
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Motwani J, Rodger EJ, Stockwell PA, Baguley BC, Macaulay EC, Eccles MR. Genome-wide DNA methylation and RNA expression differences correlate with invasiveness in melanoma cell lines. Epigenomics 2021; 13:577-598. [PMID: 33781093 DOI: 10.2217/epi-2020-0440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Aims & objectives: The aim of this study was to investigate the role of DNA methylation in invasiveness in melanoma cells. Materials & methods: The authors carried out genome-wide transcriptome (RNA sequencing) and reduced representation bisulfite sequencing methylome profiling between noninvasive (n = 4) and invasive melanoma cell lines (n = 5). Results: The integration of differentially expressed genes and differentially methylated fragments (DMFs) identified 12 DMFs (two in AVPI1, one in HMG20B, two in BCL3, one in NTSR1, one in SYNJ2, one in ROBO2 and four in HORMAD2) that overlapped with either differentially expressed genes (eight DMFs and six genes) or cis-targets of lncRNAs (five DMFs associated with cis-targets and four differentially expressed lncRNAs). Conclusions: DNA methylation changes are associated with a number of transcriptional differences observed in noninvasive and invasive phenotypes in melanoma.
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Affiliation(s)
- Jyoti Motwani
- Department of Pathology, Otago Medical School - Dunedin Campus, University of Otago, Dunedin 9054, New Zealand
| | - Euan J Rodger
- Department of Pathology, Otago Medical School - Dunedin Campus, University of Otago, Dunedin 9054, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Peter A Stockwell
- Department of Pathology, Otago Medical School - Dunedin Campus, University of Otago, Dunedin 9054, New Zealand
| | - Bruce C Baguley
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand.,Auckland Cancer Society Research Centre, The University of Auckland, Auckland 1023, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Otago Medical School - Dunedin Campus, University of Otago, Dunedin 9054, New Zealand
| | - Michael R Eccles
- Department of Pathology, Otago Medical School - Dunedin Campus, University of Otago, Dunedin 9054, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
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5
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DiseaseLinc: Disease Enrichment Analysis of Sets of Differentially Expressed LincRNAs. Cells 2021; 10:cells10040751. [PMID: 33805436 PMCID: PMC8065951 DOI: 10.3390/cells10040751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/17/2022] Open
Abstract
Long intergenic non-coding RNAs (LincRNAs) are long RNAs that do not encode proteins. Functional evidence is lacking for most of them. Their biogenesis is not well-known, but it is thought that many lincRNAs originate from genomic duplication of coding material, resulting in pseudogenes, gene copies that lose their original function and can accumulate mutations. While most pseudogenes eventually stop producing a transcript and become erased by mutations, many of these pseudogene-based lincRNAs keep similarity to the parental gene from which they originated, possibly for functional reasons. For example, they can act as decoys for miRNAs targeting the parental gene. Enrichment analysis of function is a powerful tool to discover the functional effects of a treatment producing differential expression of transcripts. However, in the case of lincRNAs, since their function is not easy to define experimentally, such a tool is lacking. To address this problem, we have developed an enrichment analysis tool that focuses on lincRNAs exploiting their functional association, using as a proxy function that of the parental genes and has a focus on human diseases.
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6
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Lister NC, Johnsson P, Waters PD, Morris KV. Pseudogenes: A Novel Source of Trans-Acting Antisense RNAs. Methods Mol Biol 2021; 2324:219-236. [PMID: 34165718 DOI: 10.1007/978-1-0716-1503-4_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Several recent studies support a functional role for pseudogenes, a copy of a parent gene that has lost protein-coding potential, which was for a long time thought to represent only "junk" DNA. Several hundreds of pseudogenes have now been reported as transcribed RNAs in a large variety of tissues and tumor types. Most studies have focused on pseudogenes expressed in sense direction, relative to their protein-coding gene counterpart, but some reports suggest that pseudogenes can be also transcribed as antisense RNAs (asRNAs). Key regulatory genes, such as PTEN and OCT4, have in fact been reported to be under the regulation of pseudogene-expressed asRNAs. Here, we review what is known about pseudogene-expressed asRNAs, we discuss the functional role that these transcripts may have in gene regulation and we summarize the techniques that are available to study them.
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Affiliation(s)
- Nicholas C Lister
- School of Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - Per Johnsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paul D Waters
- School of Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Kevin V Morris
- Menzies Health Institute and School of Pharmacology and Medical Sciences, Griffith University, Southport, QLD, Australia
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7
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Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome. Genes (Basel) 2020; 11:genes11050542. [PMID: 32408516 PMCID: PMC7290577 DOI: 10.3390/genes11050542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.
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8
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Ba MC, Ba Z, Long H, Cui SZ, Gong YF, Yan ZF, Lin KP, Wu YB, Tu YN. LncRNA AC093818.1 accelerates gastric cancer metastasis by epigenetically promoting PDK1 expression. Cell Death Dis 2020; 11:64. [PMID: 31988283 PMCID: PMC6985138 DOI: 10.1038/s41419-020-2245-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/18/2022]
Abstract
Gastric cancer (GC) is a highly prevalent type of metastatic tumor. The mechanisms underlying GC metastasis are poorly understood. Some long noncoding RNAs (lncRNAs) reportedly play key roles in regulating metastasis of GC. However, the biological roles of five natural antisense lncRNAs (AC093818.1, CTD-2541M15.1, BC047644, RP11-597M12.1, and RP11-40A13.1) in GC metastasis remain unclear. In this study, the expression of these lncRNAs was measured by quantitative reverse transcription-polymerase chain reaction. Migration and invasion were evaluated by wound-healing and the Transwell assay, respectively. Stable cells were injected into the tail veins of nude mice. Sections of collected lung and liver tissues were stained using hematoxylin and eosin. Protein expression was analyzed by western blot. RNA immunoprecipitation (RIP) assay was used to verify whether the STAT3 and SP1 transcription factors bound to AC093818.1 in GC cells. Expression levels of the five lncRNAs, especially AC093818.1, were significantly upregulated in metastatic GC tissues relative to those in nonmetastatic GC tissues. AC093818.1 expression was correlated with invasion, lymphatic metastasis, distal metastasis, and tumor-node-metastasis stage. AC093818.1 expression was highly sensitive and specific in the diagnosis of metastatic or nonmetastatic GC. AC093818.1 overexpression promoted GC migration and invasion in vitro and in vivo. AC093818.1 overexpression increased PDK1, p-AKT1, and p-mTOR expression levels. AC093818.1 silencing decreased these expressions. AC093818.1 bound to transcription factors STAT3 and SP1, and SP1 or STAT3 silencing could alleviated the effect of AC093818.1 overexpression. The data demonstrate that lncRNA AC093818.1 accelerates gastric cancer metastasis by epigenetically promoting PDK1 expression. LncRNA AC093818.1 may be a potential therapeutic target for metastatic GC.
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Affiliation(s)
- Ming-Chen Ba
- Intracelom Hyperthermic Perfusion Therapy Center, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, P.R. China.
| | - Zheng Ba
- Intensive Care Unit, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.
| | - Hui Long
- Department of Pharmacy, Guangzhou Dermatology Institute, Guangzhou, 510095, P.R. China
| | - Shu-Zhong Cui
- Intracelom Hyperthermic Perfusion Therapy Center, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, P.R. China
| | - Yuan-Feng Gong
- Intracelom Hyperthermic Perfusion Therapy Center, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, P.R. China
| | - Zhao-Fei Yan
- Intracelom Hyperthermic Perfusion Therapy Center, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, P.R. China
| | - Kun-Peng Lin
- Intracelom Hyperthermic Perfusion Therapy Center, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, P.R. China
| | - Yin-Bing Wu
- Intracelom Hyperthermic Perfusion Therapy Center, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, P.R. China
| | - Yi-Nuo Tu
- Intracelom Hyperthermic Perfusion Therapy Center, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, P.R. China
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9
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Talyan S, Andrade-Navarro MA, Muro EM. Identification of transcribed protein coding sequence remnants within lincRNAs. Nucleic Acids Res 2019; 46:8720-8729. [PMID: 29986053 PMCID: PMC6158594 DOI: 10.1093/nar/gky608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are non-coding transcripts >200 nucleotides long that do not overlap protein-coding sequences. Importantly, such elements are known to be tissue-specifically expressed and to play a widespread role in gene regulation across thousands of genomic loci. However, very little is known of the mechanisms for the evolutionary biogenesis of these RNA elements, especially given their poor conservation across species. It has been proposed that lincRNAs might arise from pseudogenes. To test this systematically, we developed a novel method that searches for remnants of protein-coding sequences within lincRNA transcripts; the hypothesis is that we can trace back their biogenesis from protein-coding genes or posterior transposon/retrotransposon insertions. Applying this method, we found 203 human lincRNA genes with regions significantly similar to protein-coding sequences. Our method provides a visualization tool to trace the evolutionary biogenesis of lincRNAs with respect to protein-coding genes by sequence divergence. Subsequently, we show the expression correlation between lincRNAs and their identified parental protein-coding genes using public RNA-seq repositories, hinting at novel gene regulatory relationships. In summary, we developed a novel computational methodology to study non-coding gene sequences, which can be applied to identify the evolutionary biogenesis and function of lincRNAs.
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Affiliation(s)
- Sweta Talyan
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
| | - Enrique M Muro
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
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10
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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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11
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Rosikiewicz W, Kabza M, Kosinski JG, Ciomborowska-Basheer J, Kubiak MR, Makalowska I. RetrogeneDB-a database of plant and animal retrocopies. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3964680. [PMID: 29220443 PMCID: PMC5509963 DOI: 10.1093/database/bax038] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/14/2017] [Indexed: 01/08/2023]
Abstract
For a long time, retrocopies were considered ‘junk DNA’, but numerous studies have shown that retrocopies may gain functionality and become so-called retrogenes. Retrogenes may code fully functional proteins that coexist with parental gene products or may even replace them. Retrocopies may also function as regulatory RNAs and, for example, become a source of small interfering RNAs, act as trans natural antisense transcripts or as alternative targets for miRNAs. Numerous researchers have emphasized that retrogenes play a crucial role in various organisms’ developmental stages and diseases. Despite the ever-growing evidence of the importance of retrocopies, resources dedicated to retroposition are very limited. Here, we report an update of the RetrogeneDB, which, to the best of our knowledge, is the largest database dedicated to retrocopies. It provides annotations of 86 458 retrocopies in 62 animal and 37 plant species. The database contains information about the retrocopies’ localization, open reading frame conservation, expression, RNA Polymerase II activity and the alternative transcription start site studies. Orthologous relationships between retrogenes were also determined, which made retrocopy conservation studies much more valuable. Additionally, based on the RNA-Seq data from the Geuvadis project, the expression levels of retrocopies were estimated in a total of 50 individuals from 5 human populations. The information is now presented in a new, more user-friendly web interface, with easy access to the source data, which may be used for the downstream analysis. RetrogeneDB is freely available at http://yeti.amu.edu.pl/retrogenedb. Database URL:http://yeti.amu.edu.pl/retrogenedb Secondary database URL:http://rhesus.amu.edu.pl/retrogenedb
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Affiliation(s)
- Wojciech Rosikiewicz
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Michal Kabza
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Jan G Kosinski
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Joanna Ciomborowska-Basheer
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Magdalena R Kubiak
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Izabela Makalowska
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
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12
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Zepeda-Mendoza CJ, Ibn-Salem J, Kammin T, Harris DJ, Rita D, Gripp KW, MacKenzie JJ, Gropman A, Graham B, Shaheen R, Alkuraya FS, Brasington CK, Spence EJ, Masser-Frye D, Bird LM, Spiegel E, Sparkes RL, Ordulu Z, Talkowski ME, Andrade-Navarro MA, Robinson PN, Morton CC. Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. Am J Hum Genet 2017; 101:206-217. [PMID: 28735859 PMCID: PMC5544382 DOI: 10.1016/j.ajhg.2017.06.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/19/2017] [Indexed: 01/08/2023] Open
Abstract
Interpretation of variants of uncertain significance, especially chromosomal rearrangements in non-coding regions of the human genome, remains one of the biggest challenges in modern molecular diagnosis. To improve our understanding and interpretation of such variants, we used high-resolution three-dimensional chromosomal structural data and transcriptional regulatory information to predict position effects and their association with pathogenic phenotypes in 17 subjects with apparently balanced chromosomal abnormalities. We found that the rearrangements predict disruption of long-range chromatin interactions between several enhancers and genes whose annotated clinical features are strongly associated with the subjects' phenotypes. We confirm gene-expression changes for a couple of candidate genes to exemplify the utility of our analysis of position effect. These results highlight the important interplay between chromosomal structure and disease and demonstrate the need to utilize chromatin conformational data for the prediction of position effects in the clinical interpretation of non-coding chromosomal rearrangements.
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Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Tammy Kammin
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David J Harris
- Harvard Medical School, Boston, MA 02115, USA; Boston Children's Hospital, Boston, MA 02115, USA
| | - Debra Rita
- Cytogenetics Lab, ACL laboratories, Rosemont, IL 60018, USA
| | - Karen W Gripp
- Nemours Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | | | - Andrea Gropman
- Children's National Medical Center, Washington, DC 20010, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Campbell K Brasington
- Clinical Genetics Division, Department of Pediatrics, Levine Children's Hospital at Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Edward J Spence
- Clinical Genetics Division, Department of Pediatrics, Levine Children's Hospital at Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Diane Masser-Frye
- Genetics and Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Lynne M Bird
- Genetics and Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA; University of California, San Diego, La Jolla, CA 92093, USA
| | - Erica Spiegel
- Maternal Fetal Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Rebecca L Sparkes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Zehra Ordulu
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael E Talkowski
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Departments of Neurology and Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Peter N Robinson
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Johannes Gutenberg University, Mainz 55122, Germany; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Centre, Manchester M13 9NT, UK.
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13
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Protein-Coding Genes' Retrocopies and Their Functions. Viruses 2017; 9:v9040080. [PMID: 28406439 PMCID: PMC5408686 DOI: 10.3390/v9040080] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.
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The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts. BMC Genomics 2015; 16:444. [PMID: 26054753 PMCID: PMC4467840 DOI: 10.1186/s12864-015-1587-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/27/2015] [Indexed: 12/13/2022] Open
Abstract
Background Natural antisense transcripts (NATs) are regulatory RNAs that contain sequence complementary to other RNAs, these other RNAs usually being messenger RNAs. In eukaryotic genomes, cis-NATs overlap the gene they complement. Results Here, our goal is to analyze the distribution and evolutionary conservation of cis-NATs for a variety of available data sets for Arabidopsis thaliana, to gain insights into cis-NAT functional mechanisms and their significance. Cis-NATs derived from traditional sequencing are largely validated by other data sets, although different cis-NAT data sets have different prevalent cis-NAT topologies with respect to overlapping protein-coding genes. A. thaliana cis-NATs have substantial conservation (28-35% in the three substantive data sets analyzed) of expression in A. lyrata. We examined evolutionary sequence conservation at cis-NAT loci in Arabidopsis thaliana across nine sequenced Brassicaceae species (picked for optimal discernment of purifying selection), focussing on the parts of their sequences not overlapping protein-coding transcripts (dubbed ‘NOLPs’). We found significant NOLP sequence conservation for 28-34% NATs across different cis-NAT sets. This NAT NOLP sequence conservation versus A. lyrata is generally significantly correlated with conservation of expression. We discover a significant enrichment of transcription factor binding sites (as evidenced by CHIP-seq data) in NOLPs compared to randomly sampled near-gene NOLP-like DNA , that is linked to significant sequence conservation. Conversely, there is no such evidence for a general significant link between NOLPs and formation of small interfering RNAs (siRNAs), with the substantial majority of unique siRNAs arising from the overlapping portions of the cis-NATs. Conclusions In aggregate, our results suggest that many cis-NAT NOLPs function in the regulation of conserved promoter/regulatory elements that they ‘over-hang’. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1587-0) contains supplementary material, which is available to authorized users.
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15
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Grandér D, Johnsson P. Pseudogene-Expressed RNAs: Emerging Roles in Gene Regulation and Disease. Curr Top Microbiol Immunol 2015; 394:111-26. [DOI: 10.1007/82_2015_442] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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16
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Characterization of human pseudogene-derived non-coding RNAs for functional potential. PLoS One 2014; 9:e93972. [PMID: 24699680 PMCID: PMC3974860 DOI: 10.1371/journal.pone.0093972] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/10/2014] [Indexed: 11/19/2022] Open
Abstract
Thousands of pseudogenes exist in the human genome and many are transcribed, but their functional potential remains elusive and understudied. To explore these issues systematically, we first developed a computational pipeline to identify transcribed pseudogenes from RNA-Seq data. Applying the pipeline to datasets from 16 distinct normal human tissues identified ∼ 3,000 pseudogenes that could produce non-coding RNAs in a manner of low abundance but high tissue specificity under normal physiological conditions. Cross-tissue comparison revealed that the transcriptional profiles of pseudogenes and their parent genes showed mostly positive correlations, suggesting that pseudogene transcription could have a positive effect on the expression of their parent genes, perhaps by functioning as competing endogenous RNAs (ceRNAs), as previously suggested and demonstrated with the PTEN pseudogene, PTENP1. Our analysis of the ENCODE project data also found many transcriptionally active pseudogenes in the GM12878 and K562 cell lines; moreover, it showed that many human pseudogenes produced small RNAs (sRNAs) and some pseudogene-derived sRNAs, especially those from antisense strands, exhibited evidence of interfering with gene expression. Further integrated analysis of transcriptomics and epigenomics data, however, demonstrated that trimethylation of histone 3 at lysine 9 (H3K9me3), a posttranslational modification typically associated with gene repression and heterochromatin, was enriched at many transcribed pseudogenes in a transcription-level dependent manner in the two cell lines. The H3K9me3 enrichment was more prominent in pseudogenes that produced sRNAs at pseudogene loci and their adjacent regions, an observation further supported by the co-enrichment of SETDB1 (a H3K9 methyltransferase), suggesting that pseudogene sRNAs may have a role in regional chromatin repression. Taken together, our comprehensive and systematic characterization of pseudogene transcription uncovers a complex picture of how pseudogene ncRNAs could influence gene and pseudogene expression, at both epigenetic and post-transcriptional levels.
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17
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Sen K, Ghosh TC. Pseudogenes and their composers: delving in the 'debris' of human genome. Brief Funct Genomics 2013; 12:536-47. [PMID: 23900003 DOI: 10.1093/bfgp/elt026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pseudogenes, the nonfunctional homologs of functional genes and thus exemplified as 'genomic fossils' provide intriguing snapshots of the evolutionary history of human genome. These defunct copies generally arise by retrotransposition or duplication followed by various genetic disablements. In this study, focusing on human pseudogenes and their functional homologues we describe their characteristic features and relevance to protein sequence evolution. We recapitulate that pseudogenes harbor disease-causing degenerative sequence variations in conjunction with the immense disease gene association of their progenitors. Furthermore, we also discuss the issue of functional resurrection and the potentiality observed in some pseudogenes to regulate their functional counterparts.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Tel.: +91 33 2355 6626; Fax: +91 33 2355 3886;
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18
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Britto-Kido SDA, Ferreira Neto JRC, Pandolfi V, Marcelino-Guimarães FC, Nepomuceno AL, Vilela Abdelnoor R, Benko-Iseppon AM, Kido EA. Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE library. ScientificWorldJournal 2013; 2013:219798. [PMID: 23878522 PMCID: PMC3710604 DOI: 10.1155/2013/219798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/05/2013] [Indexed: 11/23/2022] Open
Abstract
Natural antisense ranscripts (NAT) are RNA molecules complementary to other endogenous RNAs. They are capable of regulating the expression of target genes at different levels (transcription, mRNA stability, translation, etc.). Such a property makes them ideal for interventions in organisms' metabolism. The present study reviewed plant NAT aspects, including features, availability and genesis, conservation and distribution, coding capacity, NAT pair expression, and functions. Besides, an in silico identification of NATs pairs was presented, using deepSuperSAGE libraries of soybean infected or not with Phakopsora pachyrhizi. Results showed that around 1/3 of the 77,903 predicted trans-NATs (by PlantsNATsDB database) detected had unitags mapped in both sequences of each pair. The same 1/3 of the 436 foreseen cis-NATs showed unitags anchored in both sequences of the related pairs. For those unitags mapped in NAT pairs, a modulation expression was assigned as upregulated, downregulated, or constitutive, based on the statistical analysis (P < 0.05). As a result, the infected treatment promoted the expression of 2,313 trans-NATs pairs comprising unitags exclusively from that library (1,326 pairs had unitags only found in the mock library). To understand the regulation of these NAT pairs could be a key aspect in the ASR plant response.
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Affiliation(s)
| | | | - Valesca Pandolfi
- Federal University of Pernambuco (UFPE), Department of Genetics, Recife, PE, Brazil
| | | | - Alexandre Lima Nepomuceno
- Embrapa Soybean, Rod. Carlos João Strass, Distrito de Warta, Caixa Postal 231, 86.001-970 Londrina, PR, Brazil
| | - Ricardo Vilela Abdelnoor
- Embrapa Soybean, Rod. Carlos João Strass, Distrito de Warta, Caixa Postal 231, 86.001-970 Londrina, PR, Brazil
| | | | - Ederson Akio Kido
- Federal University of Pernambuco (UFPE), Department of Genetics, Recife, PE, Brazil
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19
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Long non-coding RNA in cancer. Int J Mol Sci 2013; 14:4655-69. [PMID: 23443164 PMCID: PMC3634483 DOI: 10.3390/ijms14034655] [Citation(s) in RCA: 283] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/03/2013] [Accepted: 01/31/2013] [Indexed: 12/31/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are pervasively transcribed in the genome and are emerging as new players in tumorigenesis due to their various functions in transcriptional, posttranscriptional and epigenetic mechanisms of gene regulation. LncRNAs are deregulated in a number of cancers, demonstrating both oncogenic and tumor suppressive roles, thus suggesting their aberrant expression may be a substantial contributor in cancer development. In this review, we will summarize their emerging role in human cancer and discuss their perspectives in diagnostics as potential biomarkers.
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20
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Knauss JL, Sun T. Regulatory mechanisms of long noncoding RNAs in vertebrate central nervous system development and function. Neuroscience 2013; 235:200-14. [PMID: 23337534 DOI: 10.1016/j.neuroscience.2013.01.022] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 12/28/2012] [Accepted: 01/09/2013] [Indexed: 01/22/2023]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as an important class of molecules that regulate gene expression at epigenetic, transcriptional, and post-transcriptional levels through a wide array of mechanisms. This regulation is of particular importance in the central nervous system (CNS), where precise modulation of gene expression is required for proper neuronal and glial production, connection and function. There are relatively few functional studies that characterize lncRNA mechanisms, but possible functions can often be inferred based on existing examples and the lncRNA's relative genomic position. In this review, we will discuss mechanisms of lncRNAs as predicted by genomic contexts and the possible impact on CNS development, function, and disease pathogenesis. There is no doubt that investigation of the mechanistic role of lncRNAs will open a new and exciting direction in studying CNS development and function.
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Affiliation(s)
- J L Knauss
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, United States.
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21
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Bray PF, McKenzie SE, Edelstein LC, Nagalla S, Delgrosso K, Ertel A, Kupper J, Jing Y, Londin E, Loher P, Chen HW, Fortina P, Rigoutsos I. The complex transcriptional landscape of the anucleate human platelet. BMC Genomics 2013; 14:1. [PMID: 23323973 PMCID: PMC3722126 DOI: 10.1186/1471-2164-14-1] [Citation(s) in RCA: 341] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022] Open
Abstract
Background Human blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide platelet RNA expression using microarrays have provided insights to the platelet transcriptome but were limited by the number of known transcripts. The goal of this effort was to deep-sequence RNA from leukocyte-depleted platelets to capture the complex profile of all expressed transcripts. Results From each of four healthy individuals we generated long RNA (≥40 nucleotides) profiles from total and ribosomal-RNA depleted RNA preparations, as well as short RNA (<40 nucleotides) profiles. Analysis of ~1 billion reads revealed that coding and non-coding platelet transcripts span a very wide dynamic range (≥16 PCR cycles beyond β-actin), a result we validated through qRT-PCR on many dozens of platelet messenger RNAs. Surprisingly, ribosomal-RNA depletion significantly and adversely affected estimates of the relative abundance of transcripts. Of the known protein-coding loci, ~9,500 are present in human platelets. We observed a strong correlation between mRNAs identified by RNA-seq and microarray for well-expressed mRNAs, but RNASeq identified many more transcripts of lower abundance and permitted discovery of novel transcripts. Conclusions Our analyses revealed diverse classes of non-coding RNAs, including: pervasive antisense transcripts to protein-coding loci; numerous, previously unreported and abundant microRNAs; retrotransposons; and thousands of novel un-annotated long and short intronic transcripts, an intriguing finding considering the anucleate nature of platelets. The data are available through a local mirror of the UCSC genome browser and can be accessed at:
http://cm.jefferson.edu/platelets_2012/.
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Affiliation(s)
- Paul F Bray
- Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
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22
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Abstract
Because they are generally noncoding and thus considered nonfunctional and unimportant, pseudogenes have long been neglected. Recent advances have established that the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes. Therefore, pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression, with a multifaceted involvement in the pathogenesis of human cancer.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori (CRL-ITT), c/o IFC-CNR Via Moruzzi 1, 56124 Pisa, Italy.
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23
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Krzyzanowski PM, Muro EM, Andrade-Navarro MA. Computational approaches to discovering noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:567-79. [PMID: 22555938 DOI: 10.1002/wrna.1121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
New developments are being brought to the field of molecular biology with the mounting evidence that RNA transcripts not translated into protein (noncoding RNAs, ncRNAs) hold a variety of biological functions. Computational discovery of ncRNAs is one of these developments, fueled not only by the urge to characterize these sequences but also by necessity to prioritize ones with the most relevant functions for experimental verification. The heterogeneity in size and mode of activity of ncRNAs is reflected in the corresponding diversity of computational methods for their study. Sequence and structural analysis, conservation across species, and relative position to other genomic elements are being used for ncRNA detection. In addition, the recent development of techniques that allow deep sequencing of cell transcripts either globally or from isolated ncRNA-related material is leading the field toward increased use of such high-throughput data. We expect that imminent breakthroughs will include the classification of newer types of ncRNA and new insights into miRNA and piRNA biology, eventually leading toward the completion of a catalog of all human ncRNAs.
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24
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Nie L, Wu HJ, Hsu JM, Chang SS, LaBaff AM, Li CW, Wang Y, Hsu JL, Hung MC. Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res 2012; 4:127-150. [PMID: 22611467 PMCID: PMC3353529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 02/16/2012] [Indexed: 06/01/2023]
Abstract
With rapid development of sequencing technologies such as deep sequencing and whole genome high-density tiling array, we now know that most of the "junk" genomic sequences are transcribed as non-coding RNAs (ncRNAs). A large number of long ncRNA transcripts (> 200bp) have been identified, and these long ncRNAs (LncRNAs) are found to be crucial regulators for epigenetic modulation, transcription, and translation. In this review, we briefly summarize the regulatory function of LncRNAs with a particular focus on the underlying mechanisms of LncRNAs in oncogenesis, tumor metastasis and suppression.
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Affiliation(s)
- Lei Nie
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
| | - Hsing-Ju Wu
- Center for Molecular Medicine, China Medical University HospitalTaichung,Taiwan
| | - Jung-Mao Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
| | - Shih-Shin Chang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
| | - Adam M LaBaff
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
| | - Chia-Wei Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
| | - Yan Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
| | - Jennifer L. Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
- Center for Molecular Medicine, China Medical University HospitalTaichung,Taiwan
- Asia UniversityTaichung, Taiwan
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center1515 Holcombe Boulevard, Houston, TX 77030
- Center for Molecular Medicine, China Medical University HospitalTaichung,Taiwan
- Graduate Institute of Cancer Biology, College of Medicine, China Medical UniversityTaichung, Taiwan
- Asia UniversityTaichung, Taiwan
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25
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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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26
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Abstract
The human septins are part of a gene family, that is a group of genes with similar sequences and usually but not invariably share similar functions that are descended from a common ancestor. Here we review our current knowledge of the human septin gene family and highlight areas of uncertainty. Currently 13 human septin genes are known (SEPT1 to SEPT12 and SEPT14). What was known as SEPT13 is now defined as one of many SEPT7 related pseudogenes. The family is characterized by complex genomics and extensive (but not universal) splicing, giving rise to a plethora of septin isoforms. For only a few members of the family do we have a comprehensive insight into these transcripts and isoforms. Given the formation of countless septin homotypic and heterotypic interactions our understanding of the biology and pathobiology of the septin family will require a detailed understanding of the genomics, transcriptomics and regulation of all members of this diverse and complex family.
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Affiliation(s)
- S E Hilary Russell
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, Northern Ireland, UK.
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27
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Muro EM, Mah N, Andrade-Navarro MA. Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie 2011; 93:1916-21. [PMID: 21816204 DOI: 10.1016/j.biochi.2011.07.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 07/19/2011] [Indexed: 11/26/2022]
Abstract
Pseudogenes have been mainly considered as functionless evolutionary relics since their discovery in 1977. However, multiple mechanisms of pseudogene functionality have been proposed both at the transcriptional and post-transcriptional level. This review focuses on the role of pseudogenes as post-transcriptional regulators. Two lines of research have recently presented strong evidence of their potential function as post-transcriptional regulators of the corresponding parental genes from which they originate. First, pseudogene genomic sequences can encode siRNAs. Second, pseudogene transcripts can act as indirect post-transcriptional regulators decoying ncRNA, in particular miRNAs that target the parental gene. This has been demonstrated for PTEN and KRAS, two genes involved in tumorigenesis. The role of pseudogenes in disease has not been proven and seems to be the next research landmark. In this review, we chronicle the events following the initial discovery of the 'useless' pseudogene to its breakthrough as a functional molecule with hitherto unbeknownst potential to influence human disease.
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Affiliation(s)
- Enrique M Muro
- Max-Delbrück Center for Molecular Medicine, Robert Rössle Str. 10, 13125 Berlin, Germany.
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28
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Piao X, Cai P, Liu S, Hou N, Hao L, Yang F, Wang H, Wang J, Jin Q, Chen Q. Global expression analysis revealed novel gender-specific gene expression features in the blood fluke parasite Schistosoma japonicum. PLoS One 2011; 6:e18267. [PMID: 21494327 PMCID: PMC3071802 DOI: 10.1371/journal.pone.0018267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/24/2011] [Indexed: 01/17/2023] Open
Abstract
Background Schistosoma japonicum is one of the remarkable
Platyhelminths that are endemic in China and Southeast Asian countries. The
parasite is dioecious and can reside inside the host for many years. Rapid
reproduction by producing large number of eggs and count-react host
anti-parasite responses are the strategies that benefit long term survival
of the parasite. Praziquantel is currently the only drug that is effective
against the worms. Development of novel antiparasite reagents and
immune-prevention measures rely on the deciphering of parasite biology. The
decoding of the genomic sequence of the parasite has made it possible to
dissect the functions of genes that govern the development of the parasite.
In this study, the polyadenylated transcripts from male and female
S. japonicum were isolated for deep sequencing and the
sequences were systematically analysed. Results First, the number of genes actively expressed in the two sexes of S.
japonicum was similar, but around 50% of genes were
biased to either male or female in expression. Secondly, it was, at the
first time, found that more than 50% of the coding region of the
genome was transcribed from both strands. Among them, 65% of the
genes had sense and their cognate antisense transcripts co-expressed,
whereas 35% had inverse relationship between sense and antisense
transcript abundance. Further, based on gene ontological analysis, more than
2,000 genes were functionally categorized and biological pathways that are
differentially functional in male or female parasites were elucidated. Conclusions Male and female schistosomal parasites differ in gene expression patterns,
many metabolic and biological pathways have been identified in this study
and genes differentially expressed in gender specific manner were presented.
Importantly, more than 50% of the coding regions of the S.
japonicum genome transcribed from both strands, antisense
RNA-mediated gene regulation might play a critical role in the parasite
biology.
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Affiliation(s)
- Xianyu Piao
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Pengfei Cai
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuai Liu
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Hou
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lili Hao
- College of Life Science and Technology,
Southwest University of Nationalities, Chengdu, Sichuan, China
| | - Fan Yang
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Heng Wang
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qijun Chen
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Zoonosis, Ministry of
Education, Institute of Zoonosis, Jilin University, Changchun, China
- * E-mail:
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