Computational biology of regulation by small RNAs

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Gene silencing and other regulatory processes guided by small RNAs are important additions to the known repertoire of biological control mechanisms. Both the total number and biological function of small RNA gene products are still largely unknown, especially in mammals. It is plausible, based on recent experiments and predictions, that there are many more non-coding RNAs than have been discovered to date and that these may be involved in regulating transcription, splicing, translation, and chromatin modification. Discovery of the complement of small RNAs, their biological functions and disease implications is therefore an important aim in molecular cell biology. Our overall aim is to help unravel the molecular details of regulatory control by small RNAs, with focus on mammals, and to develop tools for the prediction of the functional effects of this control. We will use computational means, including algorithms, software, databases and complete genome sequences, working closely with the experimental laboratories of our collaborators. We will start with the systematic and broad experimental capture of small RNA profiles and the detection and validation of target genes of small RNAs. We then plan to put small RNAs and their regulatory targets into the context of known pathways, providing a rich unified network information resource. Using this resource we will (i) analyze and predict the consequences of changes in small RNAs, their control regions and their targets, (ii) facilitate the design of focussed validation experiments and (iii) lay the foundations for the development of clinical applications. Specific areas of investigation will be the immune system and type 2 diabetes. During the course of this research, we will construct detailed regulatory networks of small RNAs and associated biological effects including: transcriptional control of small RNA production, gene silencing by translational inhibition or degradation of transcripts, and chromatin modification. We propose to organize and analyze this information in the context of the growing corpus of structured pathway data for genes, proteins, interactions and reactions in mammalian cells. For each of the specific aims we will facilitate dissemination and application of the results of the program project by making available in the public domain both software and information resources. Specific Aims: a) Profiles: Build a data annotation pipeline for small RNA profiling of mammalian cells, b) Targets: Develop computational methods for the identification and validation of the functional targets of small RNAs. c) Networks: Construct regulatory networks involving small RNAs, d) Function: Analyze the function of small RNAs and the consequences of genetic variation.