Bioinformatics analysis of small silencing RNAs
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More than 180 genomes have been deciphered, however, much remains to be learned about how genes are regulated. Transcription factors harboring promoters and distal elements are known to activate or repress downstream gene expression, and DNA methylation and histone modifications add the complexity of epigenetic regulation. Furthermore, three classes of small RNA regulators have recently been discovered to repress the target gene and transposon expression. In flies, microRNAs (miRNAs) inhibit translation and expedite degradation of the target mRNAs. Small interfering RNAs (siRNAs) participate in a self defense mechanism called RNA interference (RNAi) to silence infected virus mRNAs or endogenous transposon elements. Piwi-interaction RNAs (piRNAs) efficiently silence the transposon elements in the gonad. The advent of next generation sequencing technologies has allowed us to sequence with sufficient coverage and accuracy and perform genome-wide bioinformatics analyses on small regulatory RNAs to enrich our knowledge on regulation. In this dissertation, I developed a suite of computational algorithms and programs to study small RNAs from next generation sequencing data. First I developed a de novo miRNA discovery pipeline to discover miRNAs in sea urchin and demonstrated one of the sources of endo-siRNAs in flies was overlapping complementary mRNAs. I further investigated the question of how miRNAs and siRNAs were sorted into their own pathways. First nucleotide composition and duplex structure were shown to significantly affect the sorting protein (R2D2) to decide small RNA's destiny. Next, I described collaboration work on piRNA pathway proteins, Ago3 and Rhino. Ago3 was found to catalyze the ping-pong amplification cycle in the piRNA pathway and Rhino, a HP1 homolog, was essential for dual strand piRNA clusters. Lastly, I demonstrated a sequencing-depth independent computational approach to quantify ping-pong efficiency and illustrated the function of each piRNA pathway protein after implementing. In addition, I developed a dynamic programming for detecting piRNA clusters to better annotate the piRNAs enriched segments in the genome and revealed the expression pattern for each cluster.
Thesis (Ph.D.)--Boston UniversityPLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at firstname.lastname@example.org. Thank you.