An in-depth map of polyadenylation sites in cancer

We present a comprehensive map of over 1 million polyadenylation sites and quantify their usage in major cancers and tumor cell lines using direct RNA sequencing. We built the Expression and Polyadenylation Database to enable the visualization of the polyadenylation maps in various cancers and to facilitate the discovery of novel genes and gene isoforms that are potentially important to tumorigenesis. Analyses of polyadenylation sites indicate that a large fraction (∼30%) of mRNAs contain alternative polyadenylation sites in their 3′ untranslated regions, independent of the cell type. The shortest 3′ untranslated region isoforms are preferentially upregulated in cancer tissues, genome-wide. Candidate targets of alternative polyadenylation-mediated upregulation of short isoforms include POLR2K, and signaling cascades of cell–cell and cell–extracellular matrix contact, particularly involving regulators of Rho GTPases. Polyadenylation maps also helped to improve 3′ untranslated region annotations and identify candidate regulatory marks such as sequence motifs, H3K36Me3 and Pabpc1 that are isoform dependent and occur in a position-specific manner. In summary, these results highlight the need to go beyond monitoring only the cumulative transcript levels for a gene, to separately analysing the expression of its RNA isoforms.

[1]  T. Bailey,et al.  Inferring direct DNA binding from ChIP-seq , 2012, Nucleic acids research.

[2]  Alka A. Potdar,et al.  Coding Region Polyadenylation Generates a Truncated tRNA Synthetase that Counters Translation Repression , 2012, Cell.

[3]  Monika S. Kowalczyk,et al.  Intragenic enhancers act as alternative promoters. , 2012, Molecular cell.

[4]  Paolo Provero,et al.  Shortening of 3′UTRs Correlates with Poor Prognosis in Breast and Lung Cancer , 2012, PloS one.

[5]  M. Esteller Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.

[6]  J. Manley,et al.  Transcriptional activators enhance polyadenylation of mRNA precursors , 2011, RNA biology.

[7]  Kari Stefansson,et al.  A germline variant in the TP53 polyadenylation signal confers cancer susceptibility , 2011, Nature Genetics.

[8]  Nathan C. Sheffield,et al.  Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. , 2011, Genome research.

[9]  Wencheng Li,et al.  Transcriptional activity regulates alternative cleavage and polyadenylation , 2011, Molecular systems biology.

[10]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[11]  Yong Sun Lee,et al.  Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. , 2011, RNA.

[12]  Timothy L. Bailey,et al.  Gene expression Advance Access publication May 4, 2011 DREME: motif discovery in transcription factor ChIP-seq data , 2011 .

[13]  Chong-Jian Chen,et al.  Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing. , 2011, Genome research.

[14]  J. Turnbull,et al.  Extracellular matrix and cell signalling: the dynamic cooperation of integrin, proteoglycan and growth factor receptor. , 2011, The Journal of endocrinology.

[15]  Peter J. Shepard,et al.  Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. , 2011, RNA.

[16]  Raymond K. Auerbach,et al.  A User's Guide to the Encyclopedia of DNA Elements (ENCODE) , 2011, PLoS biology.

[17]  D. Bartel,et al.  Formation, Regulation and Evolution of Caenorhabditis elegans 3′UTRs , 2010, Nature.

[18]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[19]  J. Einasto Dark Matter , 2011, Brazilian Journal of Physics.

[20]  Francis Doyle,et al.  RIP: an mRNA localization technique. , 2011, Methods in molecular biology.

[21]  P. Sorensen,et al.  The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA , 2010, BMC Biology.

[22]  P. Kapranov,et al.  Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation , 2010, Cell.

[23]  Sebastian D. Mackowiak,et al.  The Landscape of C. elegans 3′UTRs , 2010, Science.

[24]  Nicholas T. Ingolia,et al.  Mammalian microRNAs predominantly act to decrease target mRNA levels , 2010, Nature.

[25]  Asaf Levy,et al.  Discovery of microRNAs and other small RNAs in solid tumors , 2010, Nucleic acids research.

[26]  T. Hughes,et al.  Most “Dark Matter” Transcripts Are Associated With Known Genes , 2010, PLoS biology.

[27]  Rickard Sandberg,et al.  Heterogeneity in mammalian RNA 3' end formation. , 2010, Experimental cell research.

[28]  E. Birney,et al.  A small cell lung cancer genome reports complex tobacco exposure signatures , 2009, Nature.

[29]  Job Harms,et al.  THE LANDSCAPE OF , 2010 .

[30]  B. Tian,et al.  Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types , 2009, PloS one.

[31]  J. Graber,et al.  Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes. , 2009, Cancer research.

[32]  David G Hendrickson,et al.  Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA , 2009, PLoS biology.

[33]  Jeffrey G. Reifenberger,et al.  Direct RNA sequencing , 2009, Nature.

[34]  C. Mayr,et al.  Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells , 2009, Cell.

[35]  J. Pal,et al.  Role of 5′‐ and 3′‐untranslated regions of mRNAs in human diseases , 2009, Biology of the cell.

[36]  B. Tian,et al.  Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development , 2009, Proceedings of the National Academy of Sciences.

[37]  D. Kaye,et al.  Mechanistic insights into the link between a polymorphism of the 3′UTR of the SLC7A1 gene and hypertension , 2009, Human mutation.

[38]  Melissa J. Moore,et al.  Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation , 2009, Cell.

[39]  M. Mourtada-Maarabouni,et al.  GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer , 2009, Oncogene.

[40]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..

[41]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[42]  Gabor T. Marth,et al.  Rapid whole-genome mutational profiling using next-generation sequencing technologies. , 2008, Genome research.

[43]  P. Macmathuna,et al.  NET1-mediated RhoA activation facilitates lysophosphatidic acid-induced cell migration and invasion in gastric cancer , 2008, British Journal of Cancer.

[44]  C. Lutz,et al.  Alternative polyadenylation: a twist on mRNA 3' end formation. , 2008, ACS chemical biology.

[45]  N. Rajewsky,et al.  Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.

[46]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[47]  Jun Miyoshi,et al.  Nectins and nectin-like molecules: roles in contact inhibition of cell movement and proliferation , 2008, Nature Reviews Molecular Cell Biology.

[48]  P. Sharp,et al.  Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites , 2008, Science.

[49]  John G. Collard,et al.  Rho GTPases: functions and association with cancer , 2007, Clinical & Experimental Metastasis.

[50]  Michael L. Creech,et al.  Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.

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

[52]  Adrian Wiestner,et al.  Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival. , 2007, Blood.

[53]  J. Pérez-Cañadillas Grabbing the message: structural basis of mRNA 3′UTR recognition by Hrp1 , 2006, The EMBO journal.

[54]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[55]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[56]  M. Moore From Birth to Death: The Complex Lives of Eukaryotic mRNAs , 2005, Science.

[57]  W. Filipowicz,et al.  Inhibition of Translational Initiation by Let-7 MicroRNA in Human Cells , 2005, Science.

[58]  D. Yamazaki,et al.  Regulation of cancer cell motility through actin reorganization , 2005, Cancer science.

[59]  Shuang Huang,et al.  Involvement of MicroRNA in AU-Rich Element-Mediated mRNA Instability , 2005, Cell.

[60]  A. Willis,et al.  The implications of structured 5' untranslated regions on translation and disease. , 2005, Seminars in cell & developmental biology.

[61]  Bin Tian,et al.  A large-scale analysis of mRNA polyadenylation of human and mouse genes , 2005, Nucleic acids research.

[62]  J. Hesketh,et al.  3'-Untranslated regions are important in mRNA localization and translation: lessons from selenium and metallothionein. , 2004, Biochemical Society transactions.

[63]  John Bracht,et al.  Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. , 2004, RNA.

[64]  Robert J White RNA polymerase III transcription and cancer , 2004, Oncogene.

[65]  R. White RNA polymerase III transcription--a battleground for tumour suppressors and oncogenes. , 2004, European journal of cancer.

[66]  J. Rowley,et al.  Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[67]  D Gautheret,et al.  Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. , 2001, Genome research.

[68]  E Pauws,et al.  Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. , 2001, Nucleic acids research.

[69]  J. van Helden,et al.  Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. , 2000, Nucleic acids research.

[70]  P. Thuriaux,et al.  Functional Characterization of ABC10α, an Essential Polypeptide Shared by All Three Forms of Eukaryotic DNA-dependent RNA Polymerases* , 1999, The Journal of Biological Chemistry.

[71]  R. Treisman,et al.  Activation of RhoA and SAPK/JNK signalling pathways by the RhoA‐specific exchange factor mNET1 , 1998, The EMBO journal.

[72]  Marco M. Kessler,et al.  Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3'-end formation in yeast. , 1997, Genes & development.

[73]  G. Edwalds-Gilbert,et al.  Alternative poly(A) site selection in complex transcription units: means to an end? , 1997, Nucleic acids research.

[74]  A. Sentenac,et al.  A mutation in the largest subunit of yeast TFIIIC affects tRNA and 5 S RNA synthesis. Identification of two classes of suppressors. , 1994, The Journal of biological chemistry.