A Prediction of mRNA Polyadenylation Sites in Human Genes

mRNA polyadenylation is an essential mechanism in human genes and is direct linked to the termination of transcription. Alternative polyadenylation changes the length of the mature mRNA’s 3’UTR. Since 3’UTRs have been shown to contain regulatory elements that control mRNA functioning, alternative polyadenylation plays an important role in controlling the expression of human genes. Prediction of polyadenylation sites can help with the identification of genes and aid our understanding of the mechanisms of alternative polyadenylation. In this study, we constructed a system for mRNA polyadenylation site prediction in human genes using SVM and based on an analysis of the sequence alignment between pair-end diTags (PET) and genome sequences. The PET sequences were mapped to the reference genome more accurate compared to earlier methods. We also analyzed single-site type and multiple-site type sequences PET sequence datasets and found that the frequencies of each nucleotide were different when the single-site type and multiple-site type PET sequences were compared.

[1]  J. Wilusz,et al.  Cleavage site determinants in the mammalian polyadenylation signal. , 1995, Nucleic acids research.

[2]  Ioannis P. Vlahavas,et al.  Polyadenylation site prediction using interesting emerging patterns , 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

[3]  Bin Tian,et al.  Alternative polyadenylation of cyclooxygenase-2 , 2005, Nucleic acids research.

[4]  Victor V. Solovyev,et al.  Recognition of 3'-processing sites of human mRNA precursors , 1997, Comput. Appl. Biosci..

[5]  L. Clerch,et al.  A region in the 3' UTR of MnSOD RNA enhances translation of a heterologous RNA. , 2000, Biochemical and biophysical research communications.

[6]  J. Alwine,et al.  The human immunodeficiency virus type 1 polyadenylylation signal: a 3' long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[7]  B. Cullen,et al.  Efficient polyadenylation within the human immunodeficiency virus type 1 long terminal repeat requires flanking U3-specific sequences , 1991, Journal of virology.

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

[9]  Marc Dreyfus,et al.  The Poly(A) Tail of mRNAs Bodyguard in Eukaryotes, Scavenger in Bacteria , 2002, Cell.

[10]  Robert M. Miura,et al.  Prediction of mRNA polyadenylation sites by support vector machine , 2006, Bioinform..

[11]  R. Singer,et al.  Sequences responsible for intracellular localization of beta-actin messenger RNA also affect cell phenotype , 1994, The Journal of cell biology.

[12]  Antonin Morillon,et al.  Expression of Human Fibroblast Growth Factor 2 mRNA Is Post-transcriptionally Controlled by a Unique Destabilizing Element Present in the 3′-Untranslated Region between Alternative Polyadenylation Sites* , 1999, The Journal of Biological Chemistry.

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

[14]  J. Alwine,et al.  Efficiency of utilization of the simian virus 40 late polyadenylation site: effects of upstream sequences , 1989, Molecular and cellular biology.

[15]  Jack E. Tabaska,et al.  Detection of polyadenylation signals in human DNA sequences. , 1999, Gene.

[16]  Wing-Kin Sung,et al.  PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data , 2006, BMC Bioinformatics.

[17]  L. Minvielle-Sebastia,et al.  A comparison of mammalian and yeast pre-mRNA 3'-end processing. , 1997, Current opinion in cell biology.

[18]  Jorng-Tzong Horng,et al.  RNALogo: a new approach to display structural RNA alignment , 2008, Nucleic Acids Res..

[19]  D. Gautheret,et al.  Sequence determinants in human polyadenylation site selection , 2003, BMC Genomics.

[20]  Huiqing Liu,et al.  An in-silico method for prediction of polyadenylation signals in human sequences. , 2003, Genome informatics. International Conference on Genome Informatics.

[21]  Bin Tian,et al.  PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes , 2007, Nucleic Acids Res..

[22]  T. Maniatis,et al.  An extensive network of coupling among gene expression machines , 2002, Nature.

[23]  D. Hovorun,et al.  Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. , 2003, Nucleic acids research.

[24]  Hans D. Ochs,et al.  A rare polyadenylation signal mutation of the FOXP3 gene (AAUAAA→AAUGAA) leads to the IPEX syndrome , 2001, Immunogenetics.