Biochemically informed modeling of miRNA targeting efficacy

In metazoans, microRNAs (miRNAs) are short pieces of RNA that load into Argonaute (AGO) proteins and base-pair to complementary sequences in mRNAs. Upon binding an mRNA, AGO- miRNA complexes recruit machinery that translationally represses and degrades the mRNAs. Mammalian genomes encode hundreds of miRNAs, and most mRNAs in mammals have evolutionarily conserved target sites to at least one of these miRNAs. Because of the widespread and varied roles of miRNAs in regulating gene expression, there have been many efforts over the past decade to predict the extent of targeting between a miRNA and an mRNA from their sequences alone. This targeting relationship between a miRNA and an mRNA depends on the binding affinities for the AGO-miRNA complex to target sites on the mRNA, which are poorly predicted by nearest-neighbor rules used for predicting RNA-RNA duplex stabilities.

Name thesis:degree_name

Doctoral

Department dc:contributor.department

Massachusetts Institute of Technology. Computational and Systems Biology Program

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2020

Author dc:creator

• Lin, Kathy S.

Advisor dc:contributor.advisor

• David P. Bartel.

• Computational and Systems Biology Program.

Statement dc:rights

• MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/129906

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/129906