Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data

[1]  Xiang Zhou,et al.  Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq) , 2016, Genetics.

[2]  J. Estany,et al.  Expression profiling of the GBP1 gene as a candidate gene for porcine reproductive and respiratory syndrome resistance. , 2015, Animal genetics.

[3]  Mingzhou Li,et al.  Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling , 2015, PloS one.

[4]  Shuhong Zhao,et al.  Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs , 2015, Scientific Reports.

[5]  M. Li,et al.  Comparative Anterior Pituitary miRNA and mRNA Expression Profiles of Bama Minipigs and Landrace Pigs Reveal Potential Molecular Network Involved in Animal Postnatal Growth , 2015, PloS one.

[6]  H. Ooi,et al.  Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis. , 2015, Human molecular genetics.

[7]  C. Tuggle,et al.  Transcript profiles in longissimus dorsi muscle and subcutaneous adipose tissue: a comparison of pigs with different postweaning growth rates. , 2015, Journal of animal science.

[8]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[9]  P. Hoen,et al.  Alternative mRNA transcription, processing, and translation: insights from RNA sequencing , 2015 .

[10]  Rochelle Buffenstein,et al.  Gene expression defines natural changes in mammalian lifespan , 2015, Aging cell.

[11]  Yun Ling,et al.  Transcriptomic analysis of hepatic responses to testosterone deficiency in miniature pigs fed a high-cholesterol diet , 2015, BMC Genomics.

[12]  Guoli Ji,et al.  Extraction of poly(A) sites from large-scale RNA-Seq data. , 2015, Methods in molecular biology.

[13]  P. ’. ‘t Hoen,et al.  Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. , 2015, Trends in genetics : TIG.

[14]  Hanspeter Pfister,et al.  UpSet: Visualization of Intersecting Sets , 2014, IEEE Transactions on Visualization and Computer Graphics.

[15]  Chaolin Zhang,et al.  Loss of MBNL leads to disruption of developmentally regulated alternative polyadenylation in RNA-mediated disease. , 2014, Molecular cell.

[16]  Susanna Cirera,et al.  Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model , 2014, BMC Medical Genomics.

[17]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[18]  Charles E. Determan,et al.  Fed State Prior to Hemorrhagic Shock and Polytrauma in a Porcine Model Results in Altered Liver Transcriptomic Response , 2014, PloS one.

[19]  Paul Stothard,et al.  Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding , 2014, BMC Genomics.

[20]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[21]  A. Anselmo,et al.  RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence , 2014, PloS one.

[22]  M. Groenen,et al.  Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis. , 2014, Physiological genomics.

[23]  J. Estellé,et al.  Extensive Expression Differences along Porcine Small Intestine Evidenced by Transcriptome Sequencing , 2014, PloS one.

[24]  F. Blecha,et al.  Genome-Wide Analysis of Antiviral Signature Genes in Porcine Macrophages at Different Activation Statuses , 2014, PloS one.

[25]  Jürg Bähler,et al.  Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe , 2013, RNA.

[26]  S. Bauersachs,et al.  Transcriptome Changes in the Porcine Endometrium During the Preattachment Phase1 , 2013, Biology of reproduction.

[27]  J. Estellé,et al.  Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition , 2013, BMC Genomics.

[28]  R. Bruggmann,et al.  In Search of Epigenetic Marks in Testes and Sperm Cells of Differentially Fed Boars , 2013, PloS one.

[29]  Yuan Zhang,et al.  Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars , 2013, Nature Genetics.

[30]  D. Tesfaye,et al.  RNA Deep Sequencing Reveals Novel Candidate Genes and Polymorphisms in Boar Testis and Liver Tissues with Divergent Androstenone Levels , 2013, PloS one.

[31]  J. Goeman,et al.  Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation , 2012, Nucleic acids research.

[32]  Patrice M. Milos,et al.  An in-depth map of polyadenylation sites in cancer , 2012, Nucleic acids research.

[33]  T. Babak,et al.  A quantitative atlas of polyadenylation in five mammals , 2012, Genome research.

[34]  James B. Brown,et al.  Global patterns of tissue-specific alternative polyadenylation in Drosophila. , 2012, Cell reports.

[35]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[36]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[37]  B. Futcher,et al.  The Fission Yeast RNA Binding Protein Mmi1 Regulates Meiotic Genes by Controlling Intron Specific Splicing and Polyadenylation Coupled RNA Turnover , 2011, PloS one.

[38]  Wanbo Li,et al.  A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing , 2011, BMC Genomics.

[39]  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.

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

[41]  Sylvie Doublié,et al.  Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping. , 2011, Structure.

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

[43]  X. Cui,et al.  Involvement of ER–calreticulin–Ca2+ signaling in the regulation of porcine oocyte meiotic maturation and maternal gene expression , 2010, Molecular reproduction and development.

[44]  Joseph K. Pickrell,et al.  Understanding mechanisms underlying human gene expression variation with RNA sequencing , 2010, Nature.

[45]  D. Spector,et al.  An unexpected ending: noncanonical 3' end processing mechanisms. , 2010, RNA.

[46]  X. Cui,et al.  Molecular characterization and polyadenylation‐regulated expression of cyclin B1 and Cdc2 in porcine oocytes and early parthenotes , 2010, Molecular reproduction and development.

[47]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

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

[49]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[50]  T. Jensen,et al.  The exosome: a multipurpose RNA-decay machine. , 2008, Trends in biochemical sciences.

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

[52]  Tore Samuelsson,et al.  Early evolution of histone mRNA 3' end processing. , 2007, RNA.

[53]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[54]  A. Bohm,et al.  Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis. , 2007, Structure.

[55]  Bin Tian,et al.  Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. , 2007, Genome research.

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

[57]  Diana Blank,et al.  Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination , 2002, The EMBO journal.

[58]  D. Gautheret,et al.  Patterns of variant polyadenylation signal usage in human genes. , 2000, Genome research.

[59]  T. Morozumi,et al.  Structure of the pig sterol 14alpha-demethylase (CYP51) gene and its expression in the testis and other tissues. , 2000, Journal of biochemistry.

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

[61]  S. Peltz,et al.  Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. , 1996, Annual review of biochemistry.

[62]  K. O'hare mRNA 3' ends in focus. , 1995, Trends in genetics : TIG.

[63]  E. Wahle,et al.  Poly(A) Tail Length Control Is Caused by Termination of Processive Synthesis (*) , 1995, The Journal of Biological Chemistry.

[64]  I. Mattaj,et al.  The influence of 5′ and 3′ end structures on pre-mRNA metabolism , 1995, Journal of Cell Science.

[65]  N. Proudfoot How RNA polymerase II terminates transcription in higher eukaryotes. , 1989, Trends in biochemical sciences.