Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells
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Jenny Hansson | Shamit Soneji | Göran Karlsson | Anders H. Lund | Eva Hellström-Lindberg | Mikael Sigvardsson | Stefan Lang | Cristian Bellodi | Andrew C. Hsieh | Göran Jönsson | Marios Dimitriou | A. Hsieh | G. Jönsson | M. Sigvardsson | C. Bellodi | Yiting Lim | Nicola Guzzi | M. Cieśla | P. C. T. Ngoc | S. Lang | Sonali Arora | M. Dimitriou | K. Pimková | M. Sommarin | R. Munita | M. Lubas | K. Okuyama | S. Soneji | G. Karlsson | Jenny Hansson | A. Lund | E. Hellström-Lindberg | Phuong Cao Thi Ngoc | Nicola Guzzi | Mikael N.E. Sommarin | Yiting Lim | Maciej Cieśla | Sonali Arora | Kristyna Pimková | Roberto Munita | Michal Lubas | Kazuki Okuyama | K. Pimkova | N. Guzzi | P. Ngoc | Stefan Lang
[1] Michaela Frye,et al. Stem cell function and stress response are controlled by protein synthesis , 2016, Nature.
[2] Christopher R. Sibley,et al. iCLIP: Protein–RNA interactions at nucleotide resolution , 2014, Methods.
[3] Carlos Cordon-Cardo,et al. Pten is essential for embryonic development and tumour suppression , 1998, Nature Genetics.
[4] G. Daley,et al. Telomere elongation in induced pluripotent stem cells from dyskeratosis congenita patients , 2009, Nature.
[5] Nicholas T. Ingolia,et al. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.
[6] P. Woll,et al. Perturbed hematopoietic stem and progenitor cell hierarchy in myelodysplastic syndromes patients with monosomy 7 as the sole cytogenetic abnormality , 2016, Oncotarget.
[7] Michaela Frye,et al. Role of RNA methyltransferases in tissue renewal and pathology , 2014, Current opinion in cell biology.
[8] Lluis Montoliu,et al. Genome Editing , 2018, Advances in Experimental Medicine and Biology.
[9] P. S. Ray,et al. Polysome Analysis. , 2017, Bio-protocol.
[10] Philip J. Uren,et al. Leveraging cross-link modification events in CLIP-seq for motif discovery , 2014, Nucleic acids research.
[11] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[12] Jeffrey A. Magee,et al. Haematopoietic stem cells require a highly regulated protein synthesis rate , 2014, Nature.
[13] S. Morrison,et al. Cellular Differences in Protein Synthesis Regulate Tissue Homeostasis , 2014, Cell.
[14] Lil Pabon,et al. A hierarchical network controls protein translation during murine embryonic stem cell self-renewal and differentiation. , 2008, Cell stem cell.
[15] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[16] Z. Ignatova,et al. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease , 2014, Nature Reviews Genetics.
[17] Phillipe Loher,et al. MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data , 2017, Scientific Reports.
[18] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[19] Chuan He,et al. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation , 2015, Genes & development.
[20] G. Keller,et al. Embryonic stem cell differentiation: emergence of a new era in biology and medicine. , 2005, Genes & development.
[21] W. Gilbert,et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells , 2014, Nature.
[22] N. Sonenberg,et al. Mammalian poly(A)-binding protein is a eukaryotic translation initiation factor, which acts via multiple mechanisms. , 2005, Genes & development.
[23] T. Jensen,et al. The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis. , 2015, Cell reports.
[24] Christiane Branlant,et al. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs. , 2003, RNA.
[25] B. Ebert,et al. The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia , 2016, Nature Reviews Cancer.
[26] Nian Liu,et al. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA , 2013, RNA.
[27] Ole Winther,et al. BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis , 2015, Nucleic Acids Res..
[28] G. Kozlov,et al. Interdomain allostery promotes assembly of the poly(A) mRNA complex with PABP and eIF4G. , 2012, Molecular cell.
[29] Neville E. Sanjana,et al. Improved vectors and genome-wide libraries for CRISPR screening , 2014, Nature Methods.
[30] Yi-Tao Yu,et al. RNA pseudouridylation: new insights into an old modification. , 2013, Trends in biochemical sciences.
[31] Canan Kuscu,et al. Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). , 2016, Trends in biochemical sciences.
[32] R. Tjian,et al. The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells , 2014, eLife.
[33] F. Speleman,et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.
[34] P. Ivanov,et al. Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs , 2017, Nature Communications.
[35] A. Burlingame,et al. H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation. , 2013, Cell reports.
[36] K. Shokat,et al. Genetic dissection of the oncogenic mTOR pathway reveals druggable addiction to translational control via 4EBP-eIF4E. , 2010, Cancer cell.
[37] Davide Ruggero,et al. New frontiers in translational control of the cancer genome , 2016, Nature Reviews Cancer.
[38] Maxwell R. Mumbach,et al. Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA , 2014, Cell.
[39] M. McDevitt,et al. Burst-forming unit-erythroid assays to distinguish cellular bone marrow failure disorders. , 2013, Experimental hematology.
[40] Reinout Raijmakers,et al. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics , 2009, Nature Protocols.
[41] Johan Vallon-Christersson,et al. The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs , 2009, Nature Cell Biology.
[42] J Ofengand,et al. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique. , 1993, Biochemistry.
[43] Qingfei Jiang,et al. RNA rewriting, recoding, and rewiring in human disease. , 2015, Trends in molecular medicine.
[44] Schraga Schwartz,et al. TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. , 2017, Genome research.
[45] Alberto Angrisani,et al. Human dyskerin: beyond telomeres , 2014, Biological chemistry.
[46] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[47] Davide Ruggero,et al. rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. , 2011, Molecular cell.
[48] Lisa Fish,et al. Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement , 2015, Cell.
[49] Jernej Ule,et al. NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs , 2013, Cell reports.
[50] Patricia P. Chan,et al. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes , 2015, Nucleic Acids Res..
[51] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[52] Tao Pan,et al. Dynamic RNA Modifications in Gene Expression Regulation , 2017, Cell.
[53] M. W. Gray,et al. Pseudouridine in RNA: What, Where, How, and Why , 2000, IUBMB life.
[54] J. Doudna,et al. The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.
[55] Andrew D. Smith,et al. Site identification in high-throughput RNA-protein interaction data , 2012, Bioinform..
[56] A. Jankowska,et al. Loss of heterozygosity in 7q myeloid disorders: clinical associations and genomic pathogenesis. , 2012, Blood.
[57] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[58] Joshua G. Dunn,et al. Translation from unconventional 5′ start sites drives tumour initiation , 2017, Nature.
[59] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[60] Steven P Gygi,et al. Angiogenin-induced tRNA fragments inhibit translation initiation. , 2011, Molecular cell.
[61] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[62] K. Fujii,et al. Pervasive translational regulation of the cell signalling circuitry underlies mammalian development , 2017, Nature Communications.
[63] Anne C. Rintala-Dempsey,et al. Eukaryotic stand-alone pseudouridine synthases – RNA modifying enzymes and emerging regulators of gene expression? , 2017, RNA biology.
[64] I. Behm-Ansmant,et al. RNA Sequence and Two-dimensional Structure Features Required for Efficient Substrate Modification by the Saccharomyces cerevisiae RNA:Ψ-Synthase Pus7p* , 2009, Journal of Biological Chemistry.
[65] Chengqi Yi,et al. Transcriptome-wide dynamics of RNA pseudouridylation , 2015, Nature Reviews Molecular Cell Biology.
[66] M. Mann,et al. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.
[67] Shiqing Ma,et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. , 2015, Nature chemical biology.
[68] M. Garber,et al. Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation. , 2017, Molecular cell.
[69] Arne Klungland,et al. ALKBH1-Mediated tRNA Demethylation Regulates Translation , 2016, Cell.