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Chen G, Wang C, Shi L, Qu X, Chen J, Yang J, Shi C, Chen L, Zhou P, Ning B, Tong W, Shi T. Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses. RNA (NEW YORK, N.Y.) 2013; 19:479-89. [PMID: 23431329 PMCID: PMC3677258 DOI: 10.1261/rna.037473.112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 01/14/2013] [Indexed: 05/18/2023]
Abstract
Human gene annotation is crucial for conducting transcriptomic and genetic studies; however, the impacts of human gene annotations in diverse databases on related studies have been less evaluated. To enable full use of various human annotation resources and better understand the human transcriptome, here we systematically compare the human annotations present in RefSeq, Ensembl (GENCODE), and AceView on diverse transcriptomic and genetic analyses. We found that the human gene annotations in the three databases are far from complete. Although Ensembl and AceView annotated more genes than RefSeq, more than 15,800 genes from Ensembl (or AceView) are within the intergenic and intronic regions of AceView (or Ensembl) annotation. The human transcriptome annotations in RefSeq, Ensembl, and AceView had distinct effects on short-read mapping, gene and isoform expression profiling, and differential expression calling. Furthermore, our findings indicate that the integrated annotation of these databases can obtain a more complete gene set and significantly enhance those transcriptomic analyses. We also observed that many more known SNPs were located within genes annotated in Ensembl and AceView than in RefSeq. In particular, 1033 of 3041 trait/disease-associated SNPs involved in about 200 human traits/diseases that were previously reported to be in RefSeq intergenic regions could be relocated within Ensembl and AceView genes. Our findings illustrate that a more complete transcriptome generated by incorporating human gene annotations in diverse databases can strikingly improve the overall results of transcriptomic and genetic studies.
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Affiliation(s)
- Geng Chen
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Charles Wang
- Functional Genomics Core, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Leming Shi
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Xiongfei Qu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiwei Chen
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jianmin Yang
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Caiping Shi
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Long Chen
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Peiying Zhou
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Baitang Ning
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Corresponding authorE-mail
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202
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Li W, Yang W, Wang XJ. Pseudogenes: pseudo or real functional elements? J Genet Genomics 2013; 40:171-7. [PMID: 23618400 DOI: 10.1016/j.jgg.2013.03.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 11/24/2022]
Abstract
Pseudogenes are genomic remnants of ancient protein-coding genes which have lost their coding potentials through evolution. Although broadly existed, pseudogenes used to be considered as junk or relics of genomes which have not drawn enough attentions of biologists until recent years. With the broad applications of high-throughput experimental techniques, growing lines of evidence have strongly suggested that some pseudogenes possess special functions, including regulating parental gene expression and participating in the regulation of many biological processes. In this review, we summarize some basic features of pseudogenes and their functions in regulating development and diseases. All of these observations indicate that pseudogenes are not purely dead fossils of genomes, but warrant further exploration in their distribution, expression regulation and functions. A new nomenclature is desirable for the currently called 'pseudogenes' to better describe their functions.
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Affiliation(s)
- Wen Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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203
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Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol 2013; 14:R22. [PMID: 23497673 PMCID: PMC3663115 DOI: 10.1186/gb-2013-14-3-r22] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/13/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Retroposed processed gene transcripts are an important source of material for new gene formation on evolutionary timescales. Most prior work on gene retrocopy discovery compared copies in reference genome assemblies to their source genes. Here, we explore gene retrocopy insertion polymorphisms (GRIPs) that are present in the germlines of individual humans, mice, and chimpanzees, and we identify novel gene retrocopy insertions in cancerous somatic tissues that are absent from patient-matched non-cancer genomes. RESULTS Through analysis of whole-genome sequence data, we found evidence for 48 GRIPs in the genomes of one or more humans sequenced as part of the 1,000 Genomes Project and The Cancer Genome Atlas, but which were not in the human reference assembly. Similarly, we found evidence for 755 GRIPs at distinct locations in one or more of 17 inbred mouse strains but which were not in the mouse reference assembly, and 19 GRIPs across a cohort of 10 chimpanzee genomes, which were not in the chimpanzee reference genome assembly. Many of these insertions are new members of existing gene families whose source genes are highly and widely expressed, and the majority have detectable hallmarks of processed gene retrocopy formation. We estimate the rate of novel gene retrocopy insertions in humans and chimps at roughly one new gene retrocopy insertion for every 6,000 individuals. CONCLUSIONS We find that gene retrocopy polymorphisms are a widespread phenomenon, present a multi-species analysis of these events, and provide a method for their ascertainment.
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204
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Singhal S. De novo
transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set. Mol Ecol Resour 2013; 13:403-16. [DOI: 10.1111/1755-0998.12077] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/13/2012] [Accepted: 12/22/2012] [Indexed: 01/09/2023]
Affiliation(s)
- Sonal Singhal
- Museum of Vertebrate Zoology University of California, Berkeley 3101 Valley Life Sciences Building Berkeley CA 94720‐3160 USA
- Department of Integrative Biology University of California, Berkeley 1005 Valley Life Sciences Building Berkeley CA 94720‐3140 USA
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205
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Kothari V, Wei I, Shankar S, Kalyana-Sundaram S, Wang L, Ma LW, Vats P, Grasso CS, Robinson DR, Wu YM, Cao X, Simeone DM, Chinnaiyan AM, Kumar-Sinha C. Outlier kinase expression by RNA sequencing as targets for precision therapy. Cancer Discov 2013; 3:280-93. [PMID: 23384775 DOI: 10.1158/2159-8290.cd-12-0336] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinases represent the most effective class of therapeutic targets in cancer; therefore, determination of kinase aberrations is a major focus of cancer genomic studies. Here, we analyzed transcriptome sequencing data from a compendium of 482 cancer and benign samples from 25 different tissue types, and defined distinct "outlier kinases" in individual breast and pancreatic cancer samples, based on highest levels of absolute and differential expression. Frequent outlier kinases in breast cancer included therapeutic targets like ERBB2 and FGFR4, distinct from MET, AKT2, and PLK2 in pancreatic cancer. Outlier kinases imparted sample-specific dependencies in various cell lines, as tested by siRNA knockdown and/or pharmacologic inhibition. Outlier expression of polo-like kinases was observed in a subset of KRAS-dependent pancreatic cancer cell lines, and conferred increased sensitivity to the pan-PLK inhibitor BI-6727. Our results suggest that outlier kinases represent effective precision therapeutic targets that are readily identifiable through RNA sequencing of tumors.
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Affiliation(s)
- Vishal Kothari
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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206
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Jia J, Yao P, Arif A, Fox PL. Regulation and dysregulation of 3'UTR-mediated translational control. Curr Opin Genet Dev 2013; 23:29-34. [PMID: 23312843 DOI: 10.1016/j.gde.2012.12.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/29/2012] [Accepted: 12/12/2012] [Indexed: 10/27/2022]
Abstract
Translational control provides numerous advantages in regulation of gene expression including rapid responsiveness, intracellular localization, nondestruction of template mRNA, and coordinated regulation of transcript ensembles. Transcript-selective, translational control is driven by the specific interaction of factor(s) with the 5' or 3' untranslated region (UTR), thereby influencing initiation, elongation, or termination of mRNA translation. The mean length of human 3'UTRs is greater than that of 5'UTR, indicating the expanded potential for motifs, structural elements, and binding sites for trans-acting factors that exert transcript-selective translation control. New and unexpected mechanisms of 3'UTR-mediated translational control and their contributions to disease have received increasing attention during the last decade. Here, we briefly review a few recent and representative discoveries of 3'UTR-mediated translational control, emphasizing the novel aspects of these regulatory mechanisms and their potential pathophysiological significance.
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Affiliation(s)
- Jie Jia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue/NC10, Cleveland, OH 44195, USA
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207
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O'Reilly D, Dienstbier M, Cowley SA, Vazquez P, Drozdz M, Taylor S, James WS, Murphy S. Differentially expressed, variant U1 snRNAs regulate gene expression in human cells. Genome Res 2012; 23:281-91. [PMID: 23070852 PMCID: PMC3561869 DOI: 10.1101/gr.142968.112] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human U1 small nuclear (sn)RNA, required for splicing of pre-mRNA, is encoded by genes on chromosome 1 (1p36). Imperfect copies of these U1 snRNA genes, also located on chromosome 1 (1q12-21), were thought to be pseudogenes. However, many of these "variant" (v)U1 snRNA genes produce fully processed transcripts. Using antisense oligonucleotides to block the activity of a specific vU1 snRNA in HeLa cells, we have identified global transcriptome changes following interrogation of the Affymetrix Human Exon ST 1.0 array. Our results indicate that this vU1 snRNA regulates expression of a subset of target genes at the level of pre-mRNA processing. This is the first indication that variant U1 snRNAs have a biological function in vivo. Furthermore, some vU1 snRNAs are packaged into unique ribonucleoproteins (RNPs), and many vU1 snRNA genes are differentially expressed in human embryonic stem cells (hESCs) and HeLa cells, suggesting developmental control of RNA processing through expression of different sets of vU1 snRNPs.
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Affiliation(s)
- Dawn O'Reilly
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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208
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Kabir MA, Hussain MA, Ahmad Z. Candida albicans: A Model Organism for Studying Fungal Pathogens. ISRN MICROBIOLOGY 2012; 2012:538694. [PMID: 23762753 PMCID: PMC3671685 DOI: 10.5402/2012/538694] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 08/30/2012] [Indexed: 01/12/2023]
Abstract
Candida albicans is an opportunistic human fungal pathogen that causes candidiasis. As healthcare has been improved worldwide, the number of immunocompromised patients has been increased to a greater extent and they are highly susceptible to various pathogenic microbes and C. albicans has been prominent among the fungal pathogens. The complete genome sequence of this pathogen is now available and has been extremely useful for the identification of repertoire of genes present in this pathogen. The major challenge is now to assign the functions to these genes of which 13% are specific to C. albicans. Due to its close relationship with yeast Saccharomyces cerevisiae, an edge over other fungal pathogens because most of the technologies can be directly transferred to C. albicans from S. cerevisiae and it is amenable to mutation, gene disruption, and transformation. The last two decades have witnessed enormous amount of research activities on this pathogen that leads to the understanding of host-parasite interaction, infections, and disease propagation. Clearly, C. albicans has emerged as a model organism for studying fungal pathogens along with other two fungi Aspergillus fumigatus and Cryptococcus neoformans. Understanding its complete life style of C. albicans will undoubtedly be useful for developing potential antifungal drugs and tackling Candida infections. This will also shed light on the functioning of other fungal pathogens.
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Affiliation(s)
- M Anaul Kabir
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut 673601, Kerala, India
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209
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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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210
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McCarthy N. The great pretenders. Nat Rev Cancer 2012; 12:506. [PMID: 22785353 DOI: 10.1038/nrc3326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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