Investigating the competing endogenous RNA hypothesis genome-wide and in single cells
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2015.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2015
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| Online Access: | http://hdl.handle.net/1721.1/99290 |
| _version_ | 1826201798849855488 |
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| author | Sahay, Apratim |
| author2 | Alexander van Oudenaarden and Jeff Gore. |
| author_facet | Alexander van Oudenaarden and Jeff Gore. Sahay, Apratim |
| author_sort | Sahay, Apratim |
| collection | MIT |
| description | Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2015. |
| first_indexed | 2024-09-23T11:57:05Z |
| format | Thesis |
| id | mit-1721.1/99290 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T11:57:05Z |
| publishDate | 2015 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/992902019-04-11T01:00:09Z Investigating the competing endogenous RNA hypothesis genome-wide and in single cells Investigating the competing endogenous ribonucleic acid hypothesis genome-wide and in single cells Sahay, Apratim Alexander van Oudenaarden and Jeff Gore. Massachusetts Institute of Technology. Department of Physics. Massachusetts Institute of Technology. Department of Physics. Physics. Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2015. Cataloged from PDF version of thesis. Includes bibliographical references. 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. by Apratim Sahay. Ph. D. 2015-10-14T15:03:35Z 2015-10-14T15:03:35Z 2015 2015 Thesis http://hdl.handle.net/1721.1/99290 922889626 eng M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 100, [5] pages application/pdf Massachusetts Institute of Technology |
| spellingShingle | Physics. Sahay, Apratim Investigating the competing endogenous RNA hypothesis genome-wide and in single cells |
| title | Investigating the competing endogenous RNA hypothesis genome-wide and in single cells |
| title_full | Investigating the competing endogenous RNA hypothesis genome-wide and in single cells |
| title_fullStr | Investigating the competing endogenous RNA hypothesis genome-wide and in single cells |
| title_full_unstemmed | Investigating the competing endogenous RNA hypothesis genome-wide and in single cells |
| title_short | Investigating the competing endogenous RNA hypothesis genome-wide and in single cells |
| title_sort | investigating the competing endogenous rna hypothesis genome wide and in single cells |
| topic | Physics. |
| url | http://hdl.handle.net/1721.1/99290 |
| work_keys_str_mv | AT sahayapratim investigatingthecompetingendogenousrnahypothesisgenomewideandinsinglecells AT sahayapratim investigatingthecompetingendogenousribonucleicacidhypothesisgenomewideandinsinglecells |