A web-server for detecting alternative 3'UTRs from RNA-seq experiments

Motivation:Alternativepolyadenylationhasbeenidentifiedasawidespreadmechanismin eukaryoticcellsandasanimportantstepofpost-transcriptional regulation.Protein-coding geneswithmultiplealternativepolyadenylation sitescangeneratevariouslengthsoftheir mRNA 3?UTR sequences, with the loss or gain of regulatory elements affecting stability, degradation, subcellular localization and translation. Next-generation sequencing technology (unlike previous approaches) is now able to detect variations with respect to alreadyannotatedtranscripts.InstandardRNA-seqexperimentsanddataanalysisprotocols, infact,theobtainedreconstructedtranscriptscanresultasalreadyknownorputativenovel transcript forms.Mostofthereconstructedtranscriptsentirelymatchtheannotatedones, someotherscandifferforshortorlongparts(oneormoreexons).Forthisreason,itcould be very promising a tool able to automatically detect transcripts with alternative (also putativenovel)3'untranslatedregions,shorterorlongerinspecificbiologicalconditions. Methods: We implemented a web-server called 3USS (3' Utr Sequence Seeker) to help researchers to easily retrieve 3'UTR genomic coordinates and nucleotide sequences from theprotein-codingtranscriptsreconstructedbyRNA-seqdataanalysisprotocols.Theserver accepts as input the GTF transcript file generated by procedures such as Cufflinks or Scripture (the most used tools performing the transcriptome assembly). Subsequently it compares the transcripts to the ones annotated in UCSC, NCBI, or Ensembl repositories, detecting those with diverse 3'UTR length. The data obtained from two RNA-seq experimentscanalsobeuploadedandcompared. Results: 3USS is the uniqueweb-serverable to identify RNA-seq reconstructed transcripts with3'UTRshorterorlongerthantheannotatedone.ItreturnsthefollowingResults:i)the listofthetranscripts,alongwiththelengthdifferences;ii)theputativenovel3'UTRgenomic coordinates and a multi-fasta file of the nucleotide sequences. Furthermore, it gives the possibility to compare data of two experiments, determining which transcripts share putative novel 3'UTRs in specific biological samples. These findings can be very useful to further investigate the alternative polyadenylation process, the functional role of which remainspoorlyunderstood.