TED-Seq Identifies the Dynamics of Poly(A) Length during ER Stress.

[1]  J. H. Lee,et al.  Systematic Characterization of Stress-Induced RNA Granulation. , 2018, Molecular cell.

[2]  U. Stochaj,et al.  Cytoplasmic stress granules: Dynamic modulators of cell signaling and disease. , 2017, Biochimica et biophysica acta. Molecular basis of disease.

[3]  Kyong-Tai Kim,et al.  Heterogeneous nuclear ribonucleoprotein A1 regulates rhythmic synthesis of mouse Nfil3 protein via IRES-mediated translation , 2017, Scientific Reports.

[4]  Leighton J. Core,et al.  Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) , 2016, Nature Protocols.

[5]  D. Bartel,et al.  mRNA poly(A)-tail changes specified by deadenylation broadly reshape translation in Drosophila oocytes and early embryos , 2016, eLife.

[6]  Hyeshik Chang,et al.  Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. , 2016, Molecular cell.

[7]  Anthony Barsic,et al.  ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure , 2016, Cell.

[8]  Y. Hwang,et al.  Epigenetic silencing of the MUPCDH gene as a possible prognostic biomarker for cyst growth in ADPKD , 2015, Scientific Reports.

[9]  Torsten Seemann,et al.  PAT-seq: a method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome , 2015, RNA.

[10]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[11]  F. Massi,et al.  A Conserved Three-nucleotide Core Motif Defines Musashi RNA Binding Specificity* , 2014, The Journal of Biological Chemistry.

[12]  T. Nissan,et al.  Interrelations between translation and general mRNA degradation in yeast , 2014, Wiley interdisciplinary reviews. RNA.

[13]  E. Eyras,et al.  The translational landscape of the splicing factor SRSF1 and its role in mitosis , 2014, eLife.

[14]  V. Kim,et al.  TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications. , 2014, Molecular cell.

[15]  A. MacNicol,et al.  Musashi Protein-directed Translational Activation of Target mRNAs Is Mediated by the Poly(A) Polymerase, Germ Line Development Defective-2* , 2014, The Journal of Biological Chemistry.

[16]  D. Lees-Murdock,et al.  Efficient Translation of Dnmt1 Requires Cytoplasmic Polyadenylation and Musashi Binding Elements , 2014, PloS one.

[17]  D. Bartel,et al.  Poly(A)-tail profiling reveals an embryonic switch in translational control , 2014, Nature.

[18]  A. Krainer,et al.  Isolated pseudo–RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition , 2013, Proceedings of the National Academy of Sciences.

[19]  R. Kaufman,et al.  ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death , 2013, Nature Cell Biology.

[20]  A. Quattrone,et al.  mRNA fate , 2013, RNA biology.

[21]  Leighton J. Core,et al.  Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing , 2013, Science.

[22]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[23]  N. Sonenberg,et al.  Principles of translational control: an overview. , 2012, Cold Spring Harbor perspectives in biology.

[24]  A. Bennakhi,et al.  Elevated expression of the toll like receptors 2 and 4 in obese individuals: its significance for obesity-induced inflammation , 2012, Journal of Inflammation.

[25]  N. Akimitsu,et al.  Genome-wide technology for determining RNA stability in mammalian cells , 2012, RNA biology.

[26]  J. V. Van Etten,et al.  Human Pumilio Proteins Recruit Multiple Deadenylases to Efficiently Repress Messenger RNAs* , 2012, The Journal of Biological Chemistry.

[27]  Roy Parker,et al.  P-bodies and stress granules: possible roles in the control of translation and mRNA degradation. , 2012, Cold Spring Harbor perspectives in biology.

[28]  Anna M. McGeachy,et al.  The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments , 2012, Nature Protocols.

[29]  Felice-Alessio Bava,et al.  Translational control by changes in poly(A) tail length: recycling mRNAs , 2012, Nature Structural &Molecular Biology.

[30]  B. Vojtesek,et al.  The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells. , 2012, RNA biology.

[31]  A. Giraldez,et al.  Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish , 2012, Science.

[32]  A. Komar,et al.  A Novel Feedback Loop Regulates the Response to Endoplasmic Reticulum Stress via the Cooperation of Cytoplasmic Splicing and mRNA Translation , 2012, Molecular and Cellular Biology.

[33]  P. Walter,et al.  The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation , 2011, Science.

[34]  F. Urano,et al.  Measuring ER stress and the unfolded protein response using mammalian tissue culture system. , 2011, Methods in enzymology.

[35]  G. Micklem,et al.  Poly(A) Signals Located near the 5′ End of Genes Are Silenced by a General Mechanism That Prevents Premature 3′-End Processing , 2010, Molecular and Cellular Biology.

[36]  B. Langmead,et al.  Aligning Short Sequencing Reads with Bowtie , 2010, Current protocols in bioinformatics.

[37]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[38]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[39]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[40]  H. Okano,et al.  Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP , 2008, The Journal of cell biology.

[41]  M. Wickens,et al.  Multifunctional deadenylase complexes diversify mRNA control , 2008, Nature Reviews Molecular Cell Biology.

[42]  P. Anderson,et al.  Stress granules: the Tao of RNA triage. , 2008, Trends in biochemical sciences.

[43]  F. Gebauer,et al.  Trading translation with RNA-binding proteins. , 2008, RNA.

[44]  M. Holcik,et al.  Cytoplasmic relocalization of heterogeneous nuclear ribonucleoprotein A1 controls translation initiation of specific mRNAs. , 2007, Molecular biology of the cell.

[45]  T. Gant,et al.  A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells , 2007, Nucleic acids research.

[46]  T. Preiss,et al.  Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. , 2007, RNA.

[47]  M. Holcik,et al.  Subcellular relocalization of a trans-acting factor regulates XIAP IRES-dependent translation. , 2007, Molecular biology of the cell.

[48]  Roy Parker,et al.  P bodies and the control of mRNA translation and degradation. , 2007, Molecular cell.

[49]  Sung Mi Park,et al.  BiP Internal Ribosomal Entry Site Activity Is Controlled by Heat-Induced Interaction of NSAP1 , 2006, Molecular and Cellular Biology.

[50]  J. Lykke-Andersen,et al.  Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. , 2005, Molecular cell.

[51]  M. Gorospe,et al.  Global mRNA Stabilization Preferentially Linked to Translational Repression during the Endoplasmic Reticulum Stress Response , 2004, Molecular and Cellular Biology.

[52]  M. Hentze,et al.  A poly(A) tail-responsive in vitro system for cap- or IRES-driven translation from HeLa cells. , 2004, Methods in molecular biology.

[53]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[54]  N. Gray,et al.  Regulation of mRNA translation by 5'- and 3'-UTR-binding factors. , 2003, Trends in biochemical sciences.

[55]  Vasudevan Seshadri,et al.  Translational control by the 3'-UTR: the ends specify the means. , 2003, Trends in biochemical sciences.

[56]  D. Ron,et al.  Translational control in the endoplasmic reticulum stress response. , 2002, The Journal of clinical investigation.

[57]  J. Guhaniyogi,et al.  Regulation of mRNA stability in mammalian cells. , 2001, Gene.

[58]  M. Kiledjian,et al.  The Poly(A)-Binding Protein and an mRNA Stability Protein Jointly Regulate an Endoribonuclease Activity , 2000, Molecular and Cellular Biology.

[59]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[60]  A. Krainer,et al.  Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. , 1999, Genes & development.

[61]  M. Wickens,et al.  Life and death in the cytoplasm: messages from the 3' end. , 1997, Current opinion in genetics & development.

[62]  M. Wormington Unmasking the role of the 3' UTR in the cytoplasmic polyadenylation and translational regulation of maternal mRNAs. , 1994, BioEssays : news and reviews in molecular, cellular and developmental biology.

[63]  A. Sachs,et al.  Poly(A) tail metabolism and function in eucaryotes. , 1993, The Journal of biological chemistry.

[64]  P. Cullen,et al.  Thapsigargin, a tumor promoter, discharges intracellular Ca2+ stores by specific inhibition of the endoplasmic reticulum Ca2(+)-ATPase. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Ronald W. Davis,et al.  A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability , 1987, Molecular and cellular biology.