Spt2p Defines a New Transcription-Dependent Gross Chromosomal Rearrangement Pathway

Large numbers of gross chromosomal rearrangements (GCRs) are frequently observed in many cancers. High mobility group 1 (HMG1) protein is a non-histone DNA-binding protein and is highly expressed in different types of tumors. The high expression of HMG1 could alter DNA structure resulting in GCRs. Spt2p is a non-histone DNA binding protein in Saccharomyces cerevisiae and shares homology with mammalian HMG1 protein. We found that Spt2p overexpression enhances GCRs dependent on proteins for transcription elongation and polyadenylation. Excess Spt2p increases the number of cells in S phase and the amount of single-stranded DNA (ssDNA) that might be susceptible to cause DNA damage and GCR. Consistently, RNase H expression, which reduces levels of ssDNA, decreased GCRs in cells expressing high level of Spt2p. Lastly, high transcription in the chromosome V, the location at which GCR is monitored, also enhanced GCR formation. We propose a new pathway for GCR where DNA intermediates formed during transcription can lead to genomic instability

Secondary Structures of rRNAs from All Three Domains of Life

<div><p>Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of <i>Escherichia coli, Thermus thermophilus, Haloarcula marismortui</i> (LSU rRNA only), <i>Saccharomyces cerevisiae</i>, <i>Drosophila melanogaster</i>, and <i>Homo sapiens</i>. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (<a href="http://apollo.chemistry.gatech.edu/RibosomeGallery" target="_blank">http://apollo.chemistry.gatech.edu/RibosomeGallery</a>). Mapping of data onto 2° structures was performed on the RiboVision server (<a href="http://apollo.chemistry.gatech.edu/RiboVision" target="_blank">http://apollo.chemistry.gatech.edu/RiboVision</a>).</p></div

Nested and non-nested rRNA helices.

<p>A 2° structure with four helical regions is shown in the top panel. A topology diagram, illustrating the nesting concept, is shown in the bottom panel. The green and yellow helices are nested within the red helix, with base pairs (i,q) (red) and (j,p) (yellow or green) where i</p

The 2° structure of the 16S rRNA of <i>E. coli</i>, based on three-dimensional structures.

<p>Regions where base-pairing interactions were modified relative to the co-variation 2° structure are highlighted in red. The inset shows the 2° and three-dimensional structures of the central pseudoknot (nucleotides 9–25 and 913–920). Nucleotides 9-13 are blue, nucleotides 14–19 are red, nucleotides 20–25 are green and nucleotides 913–920 are orange. The topology of the A915-U15-U20 triple is difficult to represent clearly in the 2° structure: A915 is base-paired with U15, which is base paired with U20 to form a base triple. This representation includes the sequence of the 16S rRNA and the helix and domain numbers.</p