Cis and trans-factors influence SINE genomic amplification and RNA transport
Description
Repetitive or mobile elements describe various DNA sequences that are present as multiple copies in the genomes of which they reside. In mammals, they and their recognizable remnants account for nearly half of the genome. SINEs (short interspersed nuclear elements) are the most abundant mammalian mobile elements, and amplify through an RNA intermediate in a process termed retroposition. Previous studies have demonstrated that very few individual SINEs remain retropositionally active. However, the continued amplification of these elements results in multiple negative effects, mainly through insertional mutagenesis, and unequal nonhomologous recombination events, contributing to a notable number of diseases in humans The purpose of this dissertation is to contribute to the fundamental understanding of the SINE amplification process. I present data on both RNA and protein components likely to be essential for successful SINE amplification. Chapter 2 demonstrates that a long 3' A-tail length of SINE elements may provide an advantage for inherent amplification. The youngest predicted subfamilies of rodent SINE, (ID) family elements are preferentially associated with A-tails over 50 bases in the rat genome. Another family of SINEs (rodent B1) is currently more active in mouse than in rat. Further, both the current rat ID and mouse B1 elements that are active have small, specific interruptions in their 3' A-tail sequences. My data support that these interruptions stabilize the length of the A-tails and contribute to the activity of these subfamilies The heterogeneous short RNAs produced from these SINES interact with proteins, forming RNA-protein complexes. The transcripts of the rodent BC1 RNA gene, the 'master gene' for ID amplification, are bound by protein in the form of a ribonucleoprotein particle (RNP). In chapter 3, a further characterization of the BC1 RNP is described through the use of a purification scheme with the identification of several RNP-protein candidates. Additionally, the ability of the BCl RNP to bind non-specific single-strand nucleic acid is demonstrated. Chapter 4 discusses the implications of these cis and trans-binding factors, both published and unpublished, in regard to the retroposition process, and potentially a separate neuronal function of the BC1 RNP in dendritic RNA transport