Abstract
BackgroundMicroRNAs are small highly conserved non-coding RNAs which play an important role in regulating gene expression by binding the 3'UTR of target mRNAs. The majority of microRNAs are localized within other transcriptional units (host genes) and are co-expressed with them, which strongly suggests that microRNAs and corresponding host genes use the same promoter and other expression control elements. The remaining fraction of microRNAs is intergenic and is endowed with an independent regulatory region. A number of databases have already been developed to collect information about microRNAs but none of them allow an easy exploration of microRNA genomic organization across evolution.ResultsCoGemiR is a publicly available microRNA-centered database whose aim is to offer an overview of the genomic organization of microRNAs and of its extent of conservation during evolution in different metazoan species. The database collects information on genomic location, conservation and expression data of both known and newly predicted microRNAs and displays the data by privileging a comparative point of view. The database also includes a microRNA prediction pipeline to annotate microRNAs in recently sequenced genomes. This information is easily accessible via web through a user-friendly query page. The CoGemiR database is available at ConclusionThe knowledge of the genomic organization of microRNAs can provide useful information to understand their biology. In order to have a comparative genomics overview of microRNAs genomic organization, we developed CoGemiR. To achieve this goal, we both collected and integrated data from pre-existing databases and generated new ones, such as the identification in several species of a number of previously unannotated microRNAs. For a more effective use of this data, we developed a user-friendly web interface that simply shows how a microRNA genomic context is related in different species.
Highlights
MicroRNAs are small highly conserved non-coding RNAs which play an important role in regulating gene expression by binding the 3'UTR of target mRNAs
In order to have a comparative genomics overview of microRNAs genomic organization, we developed CoGemiR
For a more effective use of this data, we developed a user-friendly web interface that shows how a microRNA genomic context is related in different species
Summary
MicroRNAs are small highly conserved non-coding RNAs which play an important role in regulating gene expression by binding the 3'UTR of target mRNAs. A number of databases have already been developed to collect information about microRNAs but none of them allow an easy exploration of microRNA genomic organization across evolution. BMC Genomics 2008, 9:457 http://www.biomedcentral.com/1471-2164/9/457 exported to the cytoplasm where they are cleaved and processed by Dicer to generate mature microRNAs [2] Concerning their genomic organization, microRNAs can be defined as a) intragenic, i.e., located within other transcriptional units (host genes), more frequently in their intronic regions and more rarely within exonic regions or b) intergenic. None of them provides all of this information simultaneously and in the context of an evolutionary perspective For this reason, we decided to develop a new microRNA-centred database with a particular focus on the genomic organization of microRNAs and of its evolutionary conservation in metazoan species
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