Investigating the competing endogenous RNA hypothesis genome-wide and in single cells
Name
922889626-MIT.pdf
Description
Full printable version
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12.29 MB
Format
Adobe PDF
Checksum (MD5)
bfb2d999b4412c174a89e63c26028aa9
Author(s)
Sahay, Apratim
Advisor(s)
Alexander van Oudenaarden and Jeff Gore.
Alternative Title
Investigating the competing endogenous ribonucleic acid hypothesis genome-wide and in single cells
Date Issued
2015
Publisher
Massachusetts Institute of Technology
Abstract
The observation that microRNAs (miRNAs), through a titration mechanism can couple interactions of their common targets (competing endogenous RNAs or ceRNAs) has prompted a general "ceRNA hypothesis" that RNAs can regulate each other indirectly through global RNA-miRNA-RNA networks. These ceRNAs are said to "crosstalk" with each other by competing for common miRNAs. Although many individual ceRNAs have been found, fundamental questions about both the magnitude and generality of the crosstalk effect remain. In our study we combine RNA sequencing and single-molecule FISH (smFISH) approaches to both measure the magnitude of the crosstalk effect genome-wide by perturbing three known ceRNAs (Pten, Vapa, Cnot6l) and to identify mechanisms by which the crosstalk effect acts. We identify hundreds of putative ceRNAs and dissect the contributions of individual miRNAs in transmitting crosstalk. We demonstrate that while the crosstalk effect is pervasive, it nevertheless remains bounded by the size of the perturbation. Furthermore, we show that both the number and affinity of shared miRNA binding sites between targets is crucial in determining the magnitude of the crosstalk strength. Using the smFISH data, we examined the single-cell gene expression profiles of pairs of ceRNAs and found that ceRNA gene expression is correlated only in the presence of active miRNAs. Additionally, on inspecting the intra-cellular localization of RNA molecules, we found a miRNA-dependent colocalization of ceRNAs, suggesting a new signature of crosstalk between ceRNAs that extends and modifies the original hypothesis.
Description
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Subjects
Physics.
MIT Department
Massachusetts Institute of Technology. Department of Physics
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