RIP-Chip: USING RNA-BINDING PROTEINS AND microRNA TARGETING TO STUDY THE HUMAN REGULATORY CODE
Scott A. Tenenbaum, PhD
Professor of Nanobioscience, College of Nanoscale Science and Engineering
The University at Albany-SUNY
Eukaryotic organisms depend on the actions of RNA-binding proteins （RBPs） for successful post-transcriptional control of gene expression. We are using methods for purifying endogenously formed RNA-Protein （RNP） complexes and identifying the associated RNA targets with microarray technologies （RIP-Chip or ribonomic profiling）. This approach has enabled the genomic-scale identification of targets of RBPs. In conjunction with the NIH/NHGRI ENCODE project we have adapted RIP-Chip profiling to tiled-microarray platforms to determine the associations of both coding and non-coding RNAs for several RBPs. This advance enabled the large-scale identification of many mRNA targets of RBPs and provided new insight into the principles governing post-transcriptional gene regulation. Our studies demonstrated that, analogous to transcriptional regulation, groups of functionally related RNAs are coordinately regulated in a combinatorial manner by distinct classes of RBPs targeting related cis-regulatory elements located in the transcripts. In addition to having significant uniqueness in exonic, intronic and novel RNA specificity, we also observe potentially important overlaps in the RNA subset affinities of the RBPs that we targeted. Presently we are using RIP-Chip to explore the post-transcriptional gene regulatory networks in stem-cell differentiation and this work will be discussed.
Our data suggests that miRNAs are modulating RBP binding sites in a dynamic manner and suggest that the cis-regulatory code targeted by miRNAs is at least in part, the same as that read by mRNA-binding proteins. This model predicts that miRNAs indirectly or directly bind to RBP binding sites. This suggests that multiple mRNA regulatory elements can simultaneously influenced by miRNA-mRNA interactions such that the binding of one or more miRNA results in conformational changes in the structure of the mRNA, thereby, either revealing or masking a second regulatory element.
By using RIP-Chip profiling to explore the post-transcriptional network, our studies suggest that in addition to targeting predicted mRNAs, many of the non-coding RNAs expressed from the genome also appear to be associated with RBPs in a specific and selective manner.
编辑: ludongcn 作者:Scott A. Tenenbaum
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