Overcoming challenges and dogmas to understand the functions of pseudogenes

[1]  S. Varambally,et al.  Pseudogene Associated Recurrent Gene Fusion in Prostate Cancer , 2019, bioRxiv.

[2]  Christopher J. F. Cameron,et al.  RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions , 2019, Nature Communications.

[3]  Catherine L. Worth,et al.  The Translational Landscape of the Human Heart , 2019, Cell.

[4]  David L. Bennett,et al.  Microdeletion in a FAAH pseudogene identified in a patient with high anandamide concentrations and pain insensitivity , 2019, British journal of anaesthesia.

[5]  Charles A Gersbach,et al.  Increasing the specificity of CRISPR systems with engineered RNA secondary structures , 2019, Nature Biotechnology.

[6]  M. Abu-Farha,et al.  PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease , 2019, Scientific Reports.

[7]  Mark Gerstein,et al.  GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..

[8]  Jacob D. Jaffe,et al.  Next-generation characterization of the Cancer Cell Line Encyclopedia , 2019, Nature.

[9]  W. Doolittle We simply cannot go on being so vague about ‘function’ , 2018, Genome Biology.

[10]  L. Patrushev,et al.  Pseudogenes as Functionally Significant Elements of the Genome , 2018, Biochemistry (Moscow).

[11]  Samira Kiani,et al.  An enhanced CRISPR repressor for targeted mammalian gene regulation , 2018, Nature Methods.

[12]  David Haussler,et al.  Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis , 2018, Cell.

[13]  David Gacquer,et al.  Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation , 2018, Cell.

[14]  A. Chen-Plotkin,et al.  The Post-GWAS Era: From Association to Function. , 2018, American journal of human genetics.

[15]  P. Concolino,et al.  Congenital Adrenal Hyperplasia (CAH) due to 21-Hydroxylase Deficiency: A Comprehensive Focus on 233 Pathogenic Variants of CYP21A2 Gene , 2018, Molecular Diagnosis & Therapy.

[16]  Daniel R. Garalde,et al.  Highly parallel direct RNA sequencing on an array of nanopores , 2016, Nature Methods.

[17]  J. Mattick,et al.  Intergenic disease-associated regions are abundant in novel transcripts , 2017, Genome Biology.

[18]  A. Brand,et al.  RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites , 2017, Nature Structural & Molecular Biology.

[19]  Michiel van Gent,et al.  Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I mediated immunity , 2017, Nature Immunology.

[20]  Nicola J. Rinaldi,et al.  Genetic effects on gene expression across human tissues , 2017, Nature.

[21]  I. Ulitsky,et al.  A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes , 2017, Genome Biology.

[22]  Bing Zhou,et al.  GRID-seq reveals the global RNA-chromatin interactome , 2017, Nature Biotechnology.

[23]  R. Hardison,et al.  Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element , 2017, Genes & development.

[24]  Phillip G. Montgomery,et al.  Defining a Cancer Dependency Map , 2017, Cell.

[25]  Z. Tsai,et al.  Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs , 2017, bioRxiv.

[26]  Jan M Skotheim,et al.  Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts , 2017, bioRxiv.

[27]  M. Oliver-Bonet,et al.  An exploratory study of predisposing genetic factors for DiGeorge/velocardiofacial syndrome , 2017, Scientific Reports.

[28]  J. Rinn,et al.  In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. , 2016, Cell reports.

[29]  Jin-Soo Kim,et al.  Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells , 2016, Nature Biotechnology.

[30]  Carolina González,et al.  SinEx DB: a database for single exon coding sequences in mammalian genomes , 2016, Database J. Biol. Databases Curation.

[31]  Martin J. Aryee,et al.  Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells , 2016, Nature Biotechnology.

[32]  Jill P. Mesirov,et al.  RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure , 2016, Cell.

[33]  Jiannis Ragoussis,et al.  Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations , 2016, Scientific Reports.

[34]  M. Dinger,et al.  Endogenous microRNA sponges: evidence and controversy , 2016, Nature Reviews Genetics.

[35]  B. Gloss,et al.  The specificity of long noncoding RNA expression. , 2016, Biochimica et biophysica acta.

[36]  A. Regev,et al.  Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins , 2015, eLife.

[37]  Xiao-Hui Zhang,et al.  Off-target Effects in CRISPR/Cas9-mediated Genome Engineering , 2015, Molecular therapy. Nucleic acids.

[38]  E. Lander,et al.  Identification and characterization of essential genes in the human genome , 2015, Science.

[39]  Z. Strezoska,et al.  Systematic analysis of CRISPR-Cas9 mismatch tolerance reveals low levels of off-target activity. , 2015, Journal of biotechnology.

[40]  E. Lyon,et al.  Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4. , 2015, The Journal of molecular diagnostics : JMD.

[41]  Thomas M. Keane,et al.  The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo , 2015, Cell.

[42]  Anton J. Enright,et al.  Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing , 2015, Nature Methods.

[43]  M. Lerch,et al.  Gene Conversion Between Cationic Trypsinogen (PRSS1) and the Pseudogene Trypsinogen 6 (PRSS3P2) in Patients with Chronic Pancreatitis , 2015, Human mutation.

[44]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

[45]  Yan Zhang,et al.  Comparative analysis of pseudogenes across three phyla , 2014, Proceedings of the National Academy of Sciences.

[46]  Wilfried Haerty,et al.  Considerations when investigating lncRNA function in vivo , 2014, eLife.

[47]  Vikram Agarwal,et al.  Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. , 2014, Molecular cell.

[48]  Gary D Bader,et al.  A draft map of the human proteome , 2014, Nature.

[49]  K. Morris,et al.  The rise of regulatory RNA , 2014, Nature Reviews Genetics.

[50]  Izabela Makałowska,et al.  RetrogeneDB—A Database of Animal Retrogenes , 2014, Molecular biology and evolution.

[51]  Geoffrey J Faulkner,et al.  Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

[52]  K. Matsumoto,et al.  The OCT4 pseudogene POU5F1B is amplified and promotes an aggressive phenotype in gastric cancer , 2013, Oncogene.

[53]  Wing Hung Wong,et al.  Characterization of the human ESC transcriptome by hybrid sequencing , 2013, Proceedings of the National Academy of Sciences.

[54]  M. Gerstein,et al.  Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division , 2013, Genome research.

[55]  Yarden Katz,et al.  Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system , 2013, Cell Research.

[56]  Howard Y. Chang,et al.  A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics , 2013, eLife.

[57]  S. Wehner,et al.  Systematic analysis and evolution of 5S ribosomal DNA in metazoans , 2013, Heredity.

[58]  R. Pink,et al.  Pseudogenes as regulators of biological function. , 2013, Essays in biochemistry.

[59]  Pedro A. F. Galante,et al.  RCPedia: a database of retrocopied genes , 2013, Bioinform..

[60]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[61]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[62]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[63]  Jennifer Doudna,et al.  RNA-programmed genome editing in human cells , 2013, eLife.

[64]  Matthew W. Hahn,et al.  Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans , 2013, PLoS genetics.

[65]  Li Ding,et al.  Retrotransposition of gene transcripts leads to structural variation in mammalian genomes , 2013, Genome Biology.

[66]  M. Gerstein,et al.  The GENCODE pseudogene resource , 2012, Genome Biology.

[67]  S. Dhanasekaran,et al.  Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers , 2012, Cell.

[68]  Anirvan Ghosh,et al.  Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation , 2012, Cell.

[69]  Peter H. Sudmant,et al.  Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication , 2012, Cell.

[70]  Brad A Chapman,et al.  The genomic binding sites of a noncoding RNA , 2011, Proceedings of the National Academy of Sciences.

[71]  Howard Y. Chang,et al.  Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. , 2011, Molecular cell.

[72]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[73]  P. Pandolfi,et al.  A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.

[74]  James C. Wright,et al.  Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. , 2011, Genome research.

[75]  E. Punch,et al.  Pseudogenes: pseudo-functional or key regulators in health and disease? , 2011, RNA.

[76]  K. Morris,et al.  Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5 , 2010, Transcription.

[77]  Henrik Kaessmann,et al.  Origins, evolution, and phenotypic impact of new genes. , 2010, Genome research.

[78]  S. Liebhaber,et al.  Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes. , 2010, Nature communications.

[79]  P. Pandolfi,et al.  A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.

[80]  J. Mattick,et al.  A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells. , 2010, RNA.

[81]  J. Mattick,et al.  Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation , 2010, BMC Neuroscience.

[82]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[83]  J. Mattick,et al.  Genome-Wide Identification of Long Noncoding RNAs in CD8+ T Cells1 , 2009, The Journal of Immunology.

[84]  J. Mattick,et al.  Long non-coding RNAs: insights into functions , 2009, Nature Reviews Genetics.

[85]  N. Goldenfeld,et al.  How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis , 2009, Microbiology and Molecular Biology Reviews.

[86]  Ran Kafri,et al.  Genetic Redundancy: New Tricks for Old Genes , 2009, Cell.

[87]  Paulo P. Amaral,et al.  MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. , 2009, Genome research.

[88]  N. Vinckenbosch,et al.  RNA-based gene duplication: mechanistic and evolutionary insights , 2009, Nature Reviews Genetics.

[89]  D. Haussler,et al.  Retrocopy contributions to the evolution of the human genome , 2008, BMC Genomics.

[90]  Paulo P. Amaral,et al.  Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. , 2008, Genome research.

[91]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[92]  S. Ranade,et al.  Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.

[93]  Y. Sakaki,et al.  Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes , 2008, Nature.

[94]  Oliver H. Tam,et al.  Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes , 2008, Nature.

[95]  S. Sunkin,et al.  Specific expression of long noncoding RNAs in the mouse brain , 2008, Proceedings of the National Academy of Sciences.

[96]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[97]  Ana Serra Barros,et al.  Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript , 2007, Nature.

[98]  Laurent Duret,et al.  The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene , 2006, Science.

[99]  Mark Gerstein,et al.  PseudoPipe: an automated pseudogene identification pipeline , 2006, Bioinform..

[100]  Annie P. Chiang,et al.  Genome‐wide identification of pseudogenes capable of disease‐causing gene conversion , 2006, Human mutation.

[101]  M. Brent,et al.  Iterative gene prediction and pseudogene removal improves genome annotation. , 2006, Genome research.

[102]  Jin Han,et al.  NANOGP8 is a retrogene expressed in cancers , 2006, The FEBS journal.

[103]  Jun Kawai,et al.  Pseudo–Messenger RNA: Phantoms of the Transcriptome , 2006, PLoS genetics.

[104]  N. Vinckenbosch,et al.  Evolutionary fate of retroposed gene copies in the human genome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[105]  M. Ingelman-Sundberg,et al.  3'-UTR polymorphism in the human CYP2A6 gene affects mRNA stability and enzyme expression. , 2006, Biochemical and biophysical research communications.

[106]  A. Reymond,et al.  Emergence of Young Human Genes after a Burst of Retroposition in Primates , 2005, PLoS biology.

[107]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[108]  Fabien Burki,et al.  Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux , 2004, Nature Genetics.

[109]  M. Gerstein,et al.  Large-scale analysis of pseudogenes in the human genome. , 2004, Current opinion in genetics & development.

[110]  J. Luban,et al.  Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1 , 2004, Nature.

[111]  G. Batist,et al.  Connexin43 pseudogene is expressed in tumor cells and inhibits growth , 2004, Oncogene.

[112]  C. Woese A New Biology for a New Century , 2004, Microbiology and Molecular Biology Reviews.

[113]  R. Stanier,et al.  The concept of a bacterium , 2004, Archiv für Mikrobiologie.

[114]  M. Suyama,et al.  A genome-wide survey of human pseudogenes. , 2003, Genome research.

[115]  Mark Gerstein,et al.  Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. , 2003, Genome research.

[116]  J. Mattick Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[117]  L. Hurst The Ka/Ks ratio: diagnosing the form of sequence evolution. , 2002, Trends in genetics : TIG.

[118]  M. Eichelbaum,et al.  Discriminative quantification of cytochrome P4502D6 and 2D7/8 pseudogene expression by TaqMan real-time reverse transcriptase polymerase chain reaction. , 2002, Analytical biochemistry.

[119]  K. Sperling,et al.  A unique form of autosomal dominant cataract explained by gene conversion between β-crystallin B2 and its pseudogene , 2001, Journal of medical genetics.

[120]  Thierry Heidmann,et al.  Human LINE retrotransposons generate processed pseudogenes , 2000, Nature Genetics.

[121]  M. O'Shea,et al.  Neuronal Expression of Neural Nitric Oxide Synthase (nNOS) Protein Is Suppressed by an Antisense RNA Transcribed from an NOS Pseudogene , 1999, The Journal of Neuroscience.

[122]  G. Germino,et al.  Gene conversion is a likely cause of mutation in PKD1. , 1998, Human molecular genetics.

[123]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[124]  J. Brosius,et al.  On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[125]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[126]  Jean-Claude Weill,et al.  Somatic hyperconversion diversifies the single VH gene of the chicken with a high incidence in the D region , 1989, Cell.

[127]  J. Weill,et al.  A hyperconversion mechanism generates the chicken light chain preimmune repertoire , 1987, Cell.

[128]  J. McCarrey Nucleotide sequence of the promoter region of a tissue-specific human retroposon: comparison with its housekeeping progenitor. , 1987, Gene.

[129]  J. McCarrey,et al.  Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene , 1987, Nature.

[130]  E. Vanin,et al.  Processed pseudogenes: characteristics and evolution. , 1984, Annual review of genetics.

[131]  G. Brownlee,et al.  A pseudogene structure in 5S DNA of Xenopus laevis , 1977, Cell.

[132]  T. Kuhn,et al.  The Structure of Scientific Revolutions. , 1964 .