Publication Date


Document Type

Doctoral Dissertation

Academic Program

Biochemistry and Molecular Pharmacology


RNA Therapeutics Institute

First Thesis Advisor

Melissa J. Moore, PhD

Second Thesis Advisor

Phillip D. Zamore, PhD


DNA, Gene Expression, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Protein Isoforms, RNA, Small Interfering RNA, DNA Sequence Analysis, Transcriptome


Dissertations, UMMS; DNA; Gene Expression; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Protein Isoforms; RNA; RNA, Small Interfering; Sequence Analysis, DNA; Transcriptome


Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets.



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