Details

Autor(en) / Beteiligte

• Freeberg, Mallory Ann

Titel

Computational analysis of the post-transcriptional gene regulatory network

Ort / Verlag

ProQuest Dissertations & Theses

Erscheinungsjahr

2015

Quelle

ProQuest Dissertations & Theses A&I

Beschreibungen/Notizen

• Across eukaryotic organisms, specific and coordinated interactions between protein-coding mRNAs, small regulatory RNAs, and a growing collection of RNA-binding proteins (RBPs) have emerged as major components orchestrating post-transcriptional gene regulation (PTGR). High-throughput sequencing technologies have dramatically accelerated our ability to probe the vast number of RNA:RNA and RBP:RNA interactions, which are the molecular drivers of PTGR. These efforts have generated an unprecedented quantity of data, placing higher demands on computational analyses to inform biological mechanisms and define underlying rules of PTGR. In this dissertation, I apply well-established computational tools and develop novel bioinformatic approaches to mine deep sequencing datasets to achieve the following aims. 1) I elucidate the biogenesis mechanism and downstream targets of the conserved piRNA class of small RNAs, which are required for fertility in Caenorhabditis elegans and higher metazoans. I define sex-specific piRNA subclasses that target unique sets of genes required for germline development. 2) I characterize the global dynamics of RBP:RNA interactions in the budding yeast Saccharomyces cerevisiae. I reveal that RBP binding explains over 40% of conservation at 3' untranslated regions, and I uncover pervasive binding of RBPs to not only single-stranded RNAs but also double-stranded RNAs, supporting a novel paradigm of RBPs targeting highly structured RNAs. Over one-third of RBP:RNA interactions are significantly altered under two environmental stress conditions, suggesting that PTGR is highly responsive to stress adaptation. 3) I identify RNA targets and propose biological mechanisms of PTGR for the conserved Pumilio family of RBPs in yeast. For example, I discovered a dual-regulatory mode of binding for Puf3p and Puf4p that is linked to both sequence and structure motifs. 4) Finally, I propose PTGR mechanisms for PUF-9- and microRNA-mediated co-regulation of developmental timing in C. elegans, and how LARP1 binding to translation machinery-encoding genes regulates mTOR signaling in human cell lines. Dysregulation of small RNA pathways and RBP-mediated processes has emerged as an important determinant in human disorders including cancer and neuromuscular disorders. Therefore, characterization of fundamental mechanisms of PTGR promises to enrich our understanding of the complex interactions governing eukaryotic gene expression and offers insights into the development of targeted therapies.