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      3USS: a web server for detecting alternative 3′UTRs from RNA-seq experiments

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          Abstract

          Summary: Protein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3′UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is a web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3 ′UTRs (shorter or longer with respect to a reference transcriptome), an option that is not available in standard RNA-seq data analysis procedures. The tool reports as putative novel the 3 ′UTRs not annotated in available databases. Furthermore, if data from two related samples are uploaded, common and specific alternative 3 ′UTRs are identified and reported by the server.

          Availability and implementation: 3USS is freely available at http://www.biocomputing.it/3uss_server

          Contact: anna.tramontano@ 123456uniroma1.it

          Supplementary information: Supplementary data are available at Bioinformatics online.

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          Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

          Mitchell Guttman, Manuel Garber, Joshua Levin … (2010)
          RNA-Seq provides an unbiased way to study a transcriptome, including both coding and non-coding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply it to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known expressed genes. We identify substantial variation in protein-coding genes, including thousands of novel 5′-start sites, 3′-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA and antisense loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes.
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            The UCSC Genome Browser database: update 2010

            Brooke Rhead, Donna Karolchik, Robert M. Kuhn … (2010)
            The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users’ own annotation data. As of September 2009, genomic sequence and a basic set of annotation ‘tracks’ are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.
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              Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development.

              Zhe Ji, Ju Youn Lee, Zhenhua Pan … (2009)
              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.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (iso-abbrev): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 01 June 2015
                Publication date (Electronic): 22 January 2015
                Publication date PMC-release: 22 January 2015
                Volume: 31
                Issue: 11
                Pages: 1845-1847
                Affiliations
                1Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, 2Department of Physics, Sapienza University, Rome, Italy and 3Istituto Pasteur – Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
                Author notes
                *To whom correspondence should be addressed.

                Associate Editor: John Hancock

                Article
                Publisher ID: btv035
                DOI: 10.1093/bioinformatics/btv035
                PMC ID: 4443675
                PubMed ID: 25617413
                SO-VID: 1f2c3b65-3130-41fe-8c9e-ee06d49cbe6f
                Copyright © © The Author 2015. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                Date received : 08 September 2014
                Date revision received : 04 December 2014
                Date accepted : 15 January 2015
                Page count
                Pages: 3
                Categories
                Subject: Applications Notes
                Subject: Gene Expression

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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