
@article{Elkon2013,
author = {Elkon, Ran and Ugalde, Alejandro P. and Agami, Reuven},
doi = {10.1038/nrg3482},
file = {:home/data/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Elkon, Ugalde, Agami - 2013 - Alternative cleavage and polyadenylation extent, regulation and function.pdf:pdf},
issn = {1471-0056},
journal = {Nature Reviews Genetics},
month = jun,
number = {7},
pages = {496--506},
publisher = {Nature Publishing Group},
title = {{Alternative cleavage and polyadenylation: extent, regulation and function}},
url = {http://www.nature.com/doifinder/10.1038/nrg3482},
volume = {14},
year = {2013}
}

@article{Cheng2006,
    abstract = {{mRNA polyadenylation is responsible for the 3' end formation of most mRNAs in eukaryotic cells and is linked to termination of transcription. Prediction of mRNA polyadenylation sites [poly(A) sites] can help identify genes, define gene boundaries, and elucidate regulatory mechanisms. Current methods for poly(A) site prediction achieve moderate sensitivity and specificity. Here, we present a method using support vector machine for poly(A) site prediction. Using 15 cis-regulatory elements that are over-represented in various regions surrounding poly(A) sites, this method achieves higher sensitivity and similar specificity when compared with polyadq, a common tool for poly(A) site prediction. In addition, we found that while the polyadenylation signal AAUAAA and U-rich elements are primary determinants for poly(A) site prediction, other elements contribute to both sensitivity and specificity of the prediction, indicating a combinatorial mechanism involving multiple elements when choosing poly(A) sites in human cells.}},
    address = {Department of Mathematical Sciences, New Jersey Institute of Technology Newark, NJ 07102, USA.},
    author = {Cheng, Y. and Miura, R. M. and Tian, B.},
    citeulike-article-id = {6332185},
    citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/16870936},
    day = {1},
    journal = {Bioinformatics},
    keywords = {analysis, mrna, ofgenomicresequencing, polya, svn},
    month = oct,
    number = {19},
    pages = {2320--2325},
    posted-at = {2009-12-06 21:30:35},
    priority = {2},
    title = {{Prediction of mRNA polyadenylation sites by support vector machine.}},
    url = {http://view.ncbi.nlm.nih.gov/pubmed/16870936},
    volume = {22},
    year = {2006}
}

@book{Fisher,
  added-at = {2009-10-28T04:42:52.000+0100},
  author = {Fisher, R.A.},
  biburl = {http://www.bibsonomy.org/bibtex/2dde0e79ae9f617d14ea8e878332febc3/jwbowers},
  date-added = {2009-08-24 14:09:49 -0500},
  date-modified = {2009-08-24 15:21:19 -0500},
  interhash = {8240df5e4c7457755487ca08fc12e870},
  intrahash = {dde0e79ae9f617d14ea8e878332febc3},
  keywords = {imported},
  publisher = {Edinburgh Oliver \& Boyd},
  timestamp = {2009-10-28T04:42:52.000+0100},
  title = {Statistical methods for research workers},
  year = 1925
}

@article{Sandberg2008,
    abstract = {{Messenger RNA (mRNA) stability, localization, and translation are largely determined by sequences in the 3′ untranslated region (3′UTR). We found a conserved increase in expression of mRNAs terminating at upstream polyadenylation sites after activation of primary murine CD4+ T lymphocytes. This program, resulting in shorter 3′UTRs, is a characteristic of gene expression during immune cell activation and correlates with proliferation across diverse cell types and tissues. Forced expression of full-length 3′UTRs conferred reduced protein expression. In some cases the reduction in protein expression could be reversed by deletion of predicted microRNA target sites in the variably included region. Our data indicate that gene expression is coordinately regulated, such that states of increased proliferation are associated with widespread reductions in the 3′UTR-based regulatory capacity of mRNAs.}},
    author = {Sandberg, Rickard and Neilson, Joel R. and Sarma, Arup and Sharp, Phillip A. and Burge, Christopher B.},
    citeulike-article-id = {2910867},
    citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1155390},
    citeulike-linkout-1 = {http://www.sciencemag.org/content/320/5883/1643.abstract},
    citeulike-linkout-2 = {http://www.sciencemag.org/content/320/5883/1643.full.pdf},
    citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/320/5883/1643},
    citeulike-linkout-4 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587246/},
    citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/18566288},
    citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=18566288},
    day = {20},
    doi = {10.1126/science.1155390},
    issn = {1095-9203},
    journal = {Science},
    keywords = {mirna, systems},
    month = jun,
    number = {5883},
    pages = {1643--1647},
    pmcid = {PMC2587246},
    pmid = {18566288},
    posted-at = {2008-08-05 10:47:55},
    priority = {2},
    publisher = {American Association for the Advancement of Science},
    title = {{Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites}},
    volume = {320},
    year = {2008}
}

@article{Mayr2009,
    abstract = {{
                In cancer cells, genetic alterations can activate proto-oncogenes, thereby contributing to tumorigenesis. However, the protein products of oncogenes are sometimes overexpressed without alteration of the proto-oncogene. Helping to explain this phenomenon, we found that when compared to similarly proliferating nontransformed cell lines, cancer cell lines often expressed substantial amounts of mRNA isoforms with shorter 3' untranslated regions (UTRs). These shorter isoforms usually resulted from alternative cleavage and polyadenylation (APA). The APA had functional consequences, with the shorter mRNA isoforms exhibiting increased stability and typically producing ten-fold more protein, in part through the loss of microRNA-mediated repression. Moreover, expression of the shorter mRNA isoform of the proto-oncogene IGF2BP1/IMP-1 led to far more oncogenic transformation than did expression of the full-length, annotated mRNA. The high incidence of APA in cancer cells, with consequent loss of 3'UTR repressive elements, suggests a pervasive role for APA in oncogene activation without genetic alteration.
            }},
    author = {Mayr, Christine and Bartel, David P.},
    citeulike-article-id = {5656121},
    citeulike-linkout-0 = {http://www.cell.com//abstract/S0092-8674(09)00716-8},
    citeulike-linkout-1 = {http://dx.doi.org/10.1016/j.cell.2009.06.016},
    citeulike-linkout-2 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819821/},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19703394},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19703394},
    day = {21},
    doi = {10.1016/j.cell.2009.06.016},
    issn = {1097-4172},
    journal = {Cell},
    keywords = {3utr, apa, journalclub, polyadenilation},
    month = aug,
    number = {4},
    pages = {673--684},
    pmcid = {PMC2819821},
    pmid = {19703394},
    posted-at = {2009-10-06 14:24:58},
    priority = {2},
    publisher = {Cell Press},
    title = {{Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells.}},
    volume = {138},
    year = {2009}
}

@article{Ji2009,
    abstract = {{
                The 3' untranslated regions (3' UTRs) of mRNAs contain cis-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3' UTRs as embryonic development progresses. This global regulation is controlled by alternative polyadenylation and coordinates with initiation of organogenesis and aspects of embryonic development, including morphogenesis, differentiation, and proliferation. Using myogenesis of C2C12 myoblast cells as a model, we recapitulated this process in vitro and found that 3' UTR lengthening is likely caused by weakening of mRNA polyadenylation activity. Because alternative 3' UTR sequences are typically longer and have higher AU content than constitutive ones, our results suggest that lengthening of 3' UTR can significantly augment posttranscriptional control of gene expression during embryonic development, such as microRNA-mediated regulation.
            }},
    author = {Ji, Zhe and Lee, Ju Y. and Pan, Zhenhua and Jiang, Bingjun and Tian, Bin},
    citeulike-article-id = {4349341},
    citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0900028106},
    citeulike-linkout-1 = {http://www.pnas.org/content/0900028106v1//.abstract},
    citeulike-linkout-2 = {http://www.pnas.org/content/0900028106v1//.full.pdf},
    citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/106/17/7028},
    citeulike-linkout-4 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669788/},
    citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/19372383},
    citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=19372383},
    day = {28},
    doi = {10.1073/pnas.0900028106},
    issn = {1091-6490},
    journal = {Proceedings of the National Academy of Sciences of the United States of America},
    keywords = {microrna, microrna-target, mrna\_profiling, polya},
    month = apr,
    number = {17},
    pages = {7028--7033},
    pmcid = {PMC2669788},
    pmid = {19372383},
    posted-at = {2010-02-15 10:26:54},
    priority = {2},
    title = {{Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development.}},
    volume = {106},
    year = {2009}
}



