Spatial preferences of microRNA targets in 3' untranslated regions

Majoros, William H; Ohler, Uwe
January 2007
BMC Genomics;2007, Vol. 8, p152
Academic Journal
Background: MicroRNAs are an important class of regulatory RNAs which repress animal genes by preferentially interacting with complementary sequence motifs in the 3′ untranslated region (UTR) of target mRNAs. Computational methods have been developed which can successfully predict which microRNA may target which mRNA on a genome-wide scale. Results: We address how predicted target sites may be affected by alternative polyadenylation events changing the 3′UTR sequence. We find that two thirds of targeted genes have alternative 3′UTRs, with 40% of predicted target sites located in alternative UTR segments. We propose three classes based on whether the target sites fall within constitutive and/or alternative UTR segments, and examine the spatial distribution of predicted targets in alternative UTRs. In particular, there is a strong preference for targets to be located in close vicinity of the stop codon and the polyadenylation sites. Conclusion: The transcript diversity seen in non-coding regions, as well as the relative location of miRNA target sites defined by it, has a potentially large impact on gene regulation by miRNAs and should be taken into account when defining, predicting or validating miRNA targets.


Related Articles

  • Molecular cloning, mRNA expression and imprinting status of PEG3, NAP1L5 and PPP1R9A genes in pig. Feng-Wei Zhang; Chang-Yan Deng; Hong-Juan He; Ning Gu; Zheng-Bin Han; Yan Chen; Qiong Wu; Shiroishi, Toshihiko // Genes & Genetic Systems;2011, Vol. 86 Issue 1, p47 

    Imprinted genes are expressed monoallelically depending on their parental origin, and play important roles in the regulation of fetal growth, development, and postnatal behavior. Most genes known to be imprinted have been identified and studied in the human and the mouse. However, there are only...

  • The RNA structurome: high-throughput probing. Westhof, Eric; Romby, Pascale // Nature Methods;Dec2010, Vol. 7 Issue 12, p965 

    The article reports that deep sequencing strategies are used to monitor the structure of cellular RNAs using enzymatic probing. It focuses on the multiple roles of RNAs in regulation of gene expression and genome stability. It states that the high throughput methods apply deep sequencing...

  • How replicable are mRNA expression QTL? Peirce, Jeremy L.; Hongqiang Li; Jintao Wang; Manly, Kenneth F.; Hitzemann, Robert J.; Belknap, John K.; Rosen, Glenn D.; Goodwin, Shirlean; Sutter, Thomas R.; Williams, Robert W.; Lu Lu // Mammalian Genome;Jun2006, Vol. 17 Issue 6, p643 

    Applying quantitative trait analysis methods to genome-wide microarray-derived mRNA expression phenotypes in segregating populations is a valuable tool in the attempt to link high-level traits to their molecular causes. The massive multiple-testing issues involved in analyzing these data make...

  • Analysis of behavior using genetical genomics in mice as a model: from alcohol preferences to gene expression differences. Singh, Shiva M.; Treadwell, Julie; Kleiber, Morgan L.; Harrison, Michelle; Uddin, Raihan K. // Genome;Oct2007, Vol. 50 Issue 10, p877 

    Most familial behavioral phenotypes result from the complex interaction of multiple genes. Studies of such phenotypes involving human subjects are often inconclusive owing to complexity of causation and experimental limitations. Studies of animal models argue for the use of established genetic...

  • Genome-wide computational identification of functional RNA elements in Trypanosoma brucei. Mao, Yuan; Najafabadi, Hamed Shateri; Salavati, Reza // BMC Genomics;2009, Vol. 10, p355 

    Background: Post-transcriptional regulation of gene expression is the dominant regulatory mechanism in trypanosomatids as their mRNAs are transcribed from polycistronic units. A few cis-acting RNA elements in 3'-untranslated regions of mRNAs have been identified in trypanosomatids, which affect...

  • A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs. Kyoungha Han; Gene Yeo; Ping An; Burge, Christopher B.; Grabowski, Paula I. // PLoS Biology;May2005, Vol. 3 Issue 5, p843 

    Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial control despite numerous sequences, distinct from splice sites, that have been shown to play...

  • RISCy business. Jabri, Evelyn // Nature Structural & Molecular Biology;Apr2004, Vol. 11 Issue 4, p300 

    Two classes of small RNAs influence a wide variety of biological processes by silencing gene expression. MicroRNAs are produced from stem-loop RNA precursors encoded in the genome and are incorporated into miRNA-induced silencing complexes. These complexes appear to silence gene expression by...

  • Sequence features associated with microRNA strand selection in humans and flies. Hai Yang Hu; Zheng Yan; Ying Xu; Hao Hu; Menzel, Corinna; Yan Hong Zhou; Wei Chen; Khaitovich, Philipp // BMC Genomics;2009, Vol. 10, p413 

    Background: During microRNA (miRNA) maturation in humans and flies, Drosha and Dicer cut the precursor transcript, thereby producing a short RNA duplex. One strand of this duplex becomes a functional component of the RNA-Induced Silencing Complex (RISC), while the other is eliminated. While...

  • On Differential Gene Expression Using RNA-Seq Data. Juhee Lee; Yuan Ji; Shoudan Liang; Guoshuai Cai; Müller, Peter // Cancer Informatics;2011, Issue 9, p205 

    Motivation: RNA-Seq is a novel technology that provides read counts of RNA fragments in each gene, including the mapped positions of each read within each gene. Besides many other applications it can be used to detect differentially expressed genes. Most published methods collapse the...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics