Tight control of gene expression is modulated by RNA binding proteins (RBPs). Transitions in post- transcriptional programs during disease and development are driven by rapid changes in the expression level of splicing factors. For example, in myotonic dystrophy type 1 (DM1) increasing disease severity corresponds to the degree of MBNL1 depletion by toxic RNA repeats. Additionally, RBFOX1, along with MBNL, are tissue- specific splicing factors, whose expression also changes significantly during the course of heart development. RBFOX proteins are also important for human embryonic stem cell survival and epithelial to mesenchymal transformation. To tune sensitivity to developmental changes in RBP levels, highly regulated RNA processing events may require moderate affinity binding sites. However, current methods for characterizing RBP preferences fail to detect these moderate affinity targets. This proposal uses high-throughput biophysical and computational techniques to identify features of RNAs targeted by two distinct families of RBPs. Deep biophysical characterization of RBFOX will identify functional elements that regulate stem cell survival and cancer. Results from these experiments will also provide a coherent description of target sequences and RNA structures that MBNL1 recognizes, ultimately providing an enhanced understanding of myotonic dystrophy pathology. The deep biophysical characterization of MBNL1 will unveil temporal transitions in RNA processing that occur with increasing DM severity. We will determine RNA affinity landscapes for MBNL1 and RBFOX to elucidate the role of RNA affinity in development and disease contexts.

Public Health Relevance

Changes in the cellular levels of RNA binding proteins (RBPs) is a hallmark of development, cancer and disease. The global identification of RNA binding affinity landscapes is required to identify functional consequences during these important post-transcriptional temporal changes.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
5F32GM101860-02
Application #
8447156
Study Section
Special Emphasis Panel (ZRG1-F08-K (20))
Program Officer
Reddy, Michael K
Project Start
2012-04-01
Project End
2015-03-31
Budget Start
2013-04-01
Budget End
2014-03-31
Support Year
2
Fiscal Year
2013
Total Cost
$52,190
Indirect Cost
Name
Massachusetts Institute of Technology
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02139