MicroRNAs (miRNAs) are a class of ～22 nt long endogenous non-coding RNAs that play important regulatory roles in diverse organisms. Up to now, little is known about the evolutionary properties of these crucial regulators. Most miRNAs were thought to be phylogenetically conserved, but recently, a number of poorly-conserved miRNAs have been reported and miRNA innovation is shown to be an ongoing process. In this work, through the characterization of an miRNA super family, we studied the evolutionary patterns of miRNAs in vertebrates. Recently generated miRNAs seem to evolve rapidly during a certain period following their emergence. Multiple lineage-specific expansions were observed. Homolgous premiRNAs may produce mature products from the opposite stem arms following tandem duplications, which may have important contribution to miRNA innovation. Our observations of miRNAs' complicated evolutionary patterns support the notion that these key regulatory molecules may play very active roles in evolution.
WANG XiaoWo, ZHANG XueGong & LI YanDa MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
Alternative translational initiation is an important mechanism to increase the diversity of gene products. Although some of alternative translational initiation events have been reported, such information remains anecdotal and does not allow for any generalizations. The number of the known alternative translational initiation genes is so few that we know little about its mechanism. There is a great demand to discover more alternative translational initiation genes. However, it is arduously time-consuming to discover novel alternative translational initiation genes by the experimental method. Therefore we systematically analyzed protein sequences available in public database and predicted 1237 protein clusters as potential alternative translational initiation events. We concluded that about 8%—10% of human genes have alternative translational initiation sites. The results significantly increased the number of alternative translation initiation events and indicated that alternative translation initiation is an important and general regulation mechanism in the cellular process.
ZHANG Jing1, CAI Jun2 & LI YanDa1 1 Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China
In recent years, much effort has been made in identifying microRNA (miRNA) genes from mammals, insects, worms, plants, and viruses. Continuing the search for more miRNA genes is still important but diffi-cult. This paper presents a computational strategy based on comparative genomics analysis. The algorithm was used to scan four invertebrate genomes, Drosophila melangoster, Bombyx mori, Apis mellifera, and Anopheles gambiae, which are either model organisms or medically/economically important insects. 99 new miRNA genes were predicted from the four insect species which can be grouped into 17 miRNA gene fami-lies, of which 10 of the miRNA families are insect-specific. Sequence similarity analysis showed that 16 of the newly predicted insect miRNAs belong to the K-box, GY-box, and Brd-box miRNA families which are impor-tant participators in Notch-related pathways. To test the validity of the algorithm, 39 predicted insect miRNA genes from D. melangoster and A. mellifera were selected for further biological validation. 34 (87%) pre-dicted miRNA genes’ transcripts were successfully detected by reverse transcription-polymerase chain reac-tion experiments. Thus, this strategy can be used to efficiently screen for miRNA genes conserved cross species.
