Our overall goal is to systematically define c/s-regulatory elements in mRNAs that control miRNA-mediated silencing under defined physiological conditions. While many miRNA targets have been predicted, and some individual targets have been investigated experimentally, the ways in which mRNA structures enhance or inhibit miRNA targeting are not known for the human transcriptome.
We aim to:
Aim 1) Map mlRNA-responsive mRNA structure in human fibroblasts.
Aim 2) Map miR-122-responsive mRNA structure in human liver cells Aim 3) Develop SHAPE-Seq for in vivo cross-validafion and analysis of mRNAs identified in Aims 1 &2.
Aim 4) Develop computafional models for predicfing miRNA target site use and efficacy. Our efforts will focus on developing validated models for miRNA binding site selecfion in human cells, with a long-term goal of coupling general properties of RNA structure to systems-level experimental constraints to enable the predicfion of miRNA targefing patterns.
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