Date of Award

1-1-2015

Language

English

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

College/School/Department

Department of Chemistry

Content Description

1 online resource (iii, 160 pages) : illustrations (some color)

Dissertation/Thesis Chair

Daniele Fabris

Committee Members

Alexander Shekhtman, Prashanth Rangan, Mehmet Yigit, Jan Halamek

Keywords

epitranscriptomics, global surveys, mass spectrometry, post-transcriptional modifications, RNomics, stress response, RNA, Non-coding RNA, Gene expression, Mass spectrometry

Subject Categories

Analytical Chemistry

Abstract

Discovery of the regulatory roles of non-protein coding RNAs (ncRNAs), once considered “junk” or “transcriptional noise”, has prompted a reassessment of the significance of the multifaceted activities of RNA in cellular response, which can result in cell transformation and diseased states. This reassessment, however, can only be accomplished if techniques are developed to capture, characterize and quantify the more than 100 covalent post-transcriptional modifications (PTMs) that adorn natural RNAs. Undoubtedly, the creation of high-throughput platforms such as next-generation sequencing and RNA-seq have provided unparalleled accuracy and sensitivity, however, they rely on strand amplification procedures that are blind to the known variants. In contrast, mass spectrometry (MS) techniques operate directly on the genuine RNA sample, not a DNA copy, and can provide the identity and sequence position of all PTMs according to their mass and fragmentation characteristics. Often, these MS approaches are coupled to a front-end separation technique such as liquid chromatography which rely on the use of standards and are ridden with sample bias and carry-over issues.

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