Bioinformatic Analysis Of MicroRNA Related Key Proteins In Animal Genomes

Non-coding RNA (ncRNA) genes produce functional RNA molecules rather than encoding proteins. Non-coding RNAs are emerging as central players in gene expression regulation. MicroRNAs are ~22 nt long small non-coding RNAs that play important regulatory roles in eukaryotes. MicroRNAs involve in the regulation of many important biological processes, such as cell proliferation and differentiation, developmental timing and organ formation, signal transduction and the development of some diseases, especially certain cancers, and also growth control, stress response and antiviral defense. The founding member of microRNAs, lin-4, was first identified in C. elegans in 1993. And microRNAs were given systematic naming standard in 2001. Many microRNAs from aminals, plants and viruses have been identified to this day. Till March 2009, the miRBase Sequence Database from the famous Sanger Institute contained 9539 entried representing hairpin precursor microRNAs, expressing 9169 mature microRNA products in 103 species.The research on microRNAs has been a new field and hot spot of biological research.The biogenesis process of microRNAs in animals requires the participation of many proteins, of which, the well studied ones are Dicer, Drosha, Argonaute and Exportin 5. To systematically study these four protein families, we screened 11 animal genomes, including C.elegans, Drosophila, Zebrafish, chicken, platypus, cow, horse, dog, mouse, rat and human, to study genes encoding above mentioned proteins and their important properties.The main researches contained numbers of each protein family, their domain components, alternative splicing phenomenon, nuclear localization signal, the interaction between these genes and microRNAs, the expression and regulation pattern and interactions between these proteins and other ones.The results of this research included the following aspects.1) Identified some new members for each protein family.2) Constructed the phylogenetic trees of Drosha, Dicer, Argonaute and Exportin 5 protein families among different species.3) Clarified domains of these proteins and the domain analysis results revealed that most proteins within the same family share identical or similar domains.4) Alternatively spliced transcript variants were found for some proteins. 5) Identified the nuclear localization signal sequences in Argonaute protein families.6) Predicted the target sequences of microRNAs in the four protein families among 11 species.7) Examined the expression patterns of these proteins in different human tissues and identified other proteins that could potentially interact with these proteins.These findings provided systematic information on the four key proteins in animal microRNA biogenesis pathway, will shed light on further functional studies of these proteins.