Development and Application of Proteomic and Genomic Methods in RNA Biology

Citation

Honson, Drew D. (2025) Development and Application of Proteomic and Genomic Methods in RNA Biology. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/08dq-1q63. https://resolver.caltech.edu/CaltechTHESIS:12092024-181948039

Abstract

This thesis contains three interrelated projects. Chapter 1 describes the development of a novel RNA-proteomics method: RNA-antisense purification followed by mass spectrometry (RAP-MS 2.0). It contains results of a RAP-MS 2.0 study profiling the protein partners of eight RNAs (7SL, 7SK, RMRP, U1, U2, U6, U7, and Xist) as well as a detailed, step-by-step protocol for the new method. Chapter 2 describes a quality control method for Split and Pool Identification of RBP targets (SPIDR). It identifies an underappreciated failure point in SPIDR experiments (the equal loading of antibody-IDs onto beads), and describes a method for monitoring and resolving this issue. Chapter 3 describes the application of SPIDR to ribosome-associated proteins in human cells. The study both validates existing structures and identifies novel interactions between nucleolar proteins and immature ribosomal RNA, and between protein trafficking factors and the large ribosomal subunit.

Item Type:

Thesis (Dissertation (Ph.D.))

Subject Keywords:

RNA;proteomics;genomics;u1;xist;ribosome;spidr;rapms;rap-ms

Degree Grantor:

California Institute of Technology

Division:

Biology and Biological Engineering

Major Option:

Biology

Thesis Availability:

Not set

Research Advisor(s):

Guttman, Mitchell

Thesis Committee:

Elowitz, Michael B. (chair)
Fejes Toth, Katalin
Zernicka-Goetz, Magdalena
Guttman, Mitchell

Defense Date:

3 December 2024

Funders:

Funding Agency	Grant Number
National Institutes of Health (NIH)	1U01DK127420-01

Record Number:

CaltechTHESIS:12092024-181948039

Persistent URL:

https://resolver.caltech.edu/CaltechTHESIS:12092024-181948039

DOI:

10.7907/08dq-1q63

ORCID:

Author	ORCID
Honson, Drew D.	0000-0002-4654-8974

Default Usage Policy:

No commercial reproduction, distribution, display or performance rights in this work are provided.

ID Code:

16911

Collection:

CaltechTHESIS

Deposited By:

Drew Honson

Deposited On:

12 Feb 2025 23:43

Last Modified:

12 Feb 2025 23:43

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