Telomeric sequence diversity within the genus Saccharomyces

Broken chromosomes healed by de novo addition of a telomere are a major class of genome rearrangements seen in Saccharomyces cerevisiae and similar to rearrangements seen in human tumors. We have analyzed the sequences of 534 independent de novo telomere additions within a 12-kb region of chromosome V. The distribution of events mirrored that of four-base sequences consisting of the GG, GT, and TG dinucleotides, suggesting that de novo telomere additions occur at short regions of homology to the telomerase guide RNA. These chromosomal sequences restrict potential registrations of the added telomere sequence. The first 11 nucleotides of the addition sequences fell into common families that included 91% of the breakpoints. The observed registrations suggest that the 3 end of the TLC1 guide RNA is involved in annealing but not as a template for synthesis. Some families of added sequences can be accounted for by one cycle of annealing and extension, whereas others require a minimum of two. The same pattern emerges for sequences added onto the most common addition sequence, indicating that de novo telomeres are added and extended by the same process. Together, these data indicate that annealing is central to telomerase registration, which limits telomere heterogeneity and resolves the problem of synthesizing Rap1 binding sites by a nonprocessive telomerase with a lowcomplexity guide RNA sequence.

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Chromosome healing through terminal deletions generated by de novo telomere additions in Saccharomyces cerevisiae

Putnam

Pennaneach

Kolodner

2004

“…Rap1p's binding specificity is associated with its ancient and conserved function in the regulation of telomere length (15). The RAP1 binding site in RP promoters is a submotif of the telomeric repeat sequence bound by Rap1p in these species (16), including those that do not have a RAP1 site in their RP promoters. Thus, the sequence of the RAP1 motif that emerged in RP promoters matched Rap1p's preexisting DNA binding site.…”

Section: Orthologous Transcriptional Modulesmentioning

confidence: 99%

Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast

Tanay

Regev

Shamir

2005

245

254

Transcriptional modules of coregulated genes play a key role in regulatory networks. Comparative studies show that modules of coexpressed genes are conserved across taxa. However, little is known about the mechanisms underlying the evolution of module regulation. Here, we explore the evolution of cis-regulatory programs associated with conserved modules by integrating expression profiles for two yeast species and sequence data for a total of 17 fungal genomes. We show that although the cis-elements accompanying certain conserved modules are strictly conserved, those of other conserved modules are remarkably diverged. In particular, we infer the evolutionary history of the regulatory program governing ribosomal modules. We show how a ciselement emerged concurrently in dozens of promoters of ribosomal protein genes, followed by the loss of a more ancient cis-element. We suggest that this formation of an intermediate redundant regulatory program allows conserved transcriptional modules to gradually switch from one regulatory mechanism to another while maintaining their functionality. Our work provides a general framework for the study of the dynamics of promoter evolution at the level of transcriptional modules and may help in understanding the evolvability and increased redundancy of transcriptional regulation in higher organisms.regulatory motifs ͉ transcriptional networks T ranscriptional modules, i.e., groups of coregulated genes, play a central role in the organization and function of regulatory networks (1-3). Comparative studies have demonstrated that various transcriptional modules are highly conserved across a wide variety of organisms from Escherichia coli to humans (4-6). A common tacit assumption is that conserved regulatory mechanisms underlie module conservation, because coregulation imposes tight constraints on the evolution of a module's promoters. Indeed, recent studies showed that orthologous transcriptional modules are often associated with conserved cis-elements (7).To gain new insights into the evolution of regulation of transcriptional modules, we developed an integrated method for comparative expression and sequence analysis. We applied our method to 17 fully sequenced yeast genomes and identified conserved transcriptional modules and the cis-elements that are associated with them in each species. Although the cis-elements associated with certain modules were conserved in all species, other modules were associated with distinct cis-elements in different species. Divergence of cis-elements in specific promoters has been documented, e.g., in refs. 8 and 9, but it is difficult to explain in a similar way the divergence we observed in a regulatory program associated with dozens of coexpressed genes. In particular, it is not clear how multiple promoters diverge in a coordinated way and how divergence occurs without adversely affecting the coexpression phenotype. To answer this question, we inferred the detailed evolutionary history of modules' regulatory programs and studied different evolutionary...

“…Rap1 is an essential protein that binds yeast telomeric DNA and negatively regulates telomere length. Sites for Rap1 binding are conserved among the telomeric sequences of budding yeasts, despite wide interspecies variation in both the size and sequence of unit telomeric repeats (12). By mutating the template region of the gene encoding the RNA subunit of telomerase, we engineered cells with mutant repeats added to the termini of all telomeres.…”

mentioning

confidence: 99%

Telomere fusions caused by mutating the terminal region of telomeric DNA

McEachern

Iyer

Fulton

et al. 2000

Self Cite

Mutations in the template region of a telomerase RNA gene can lead to the corresponding sequence alterations appearing in newly synthesized telomeric repeats. We analyzed a set of mutations in the template region of the telomerase RNA gene (TER1) of the budding yeast Kluyveromyces lactis that were predicted to lead to synthesis of mutant telomeric repeats with disrupted binding of the telomeric protein Rap1p. We showed previously that mutating the left side of the 12-bp consensus Rap1p binding site led to immediate and severe telomere elongation. Here, we show that, in contrast, mutating either the right side of the site or both sides together leads initially to telomere shortening. On additional passaging, certain mutants of both categories exhibit telomeretelomere fusions. Often, six new Bal-31-resistant, telomere repeatcontaining bands appeared, and we infer that each of the six K. lactis chromosomes became circularized. These fusions were not stable, appearing occasionally to resolve and then reform. We demonstrate directly that a linear minichromosome introduced into one of the fusion mutant strains circularized by means of end-to-end fusions of the mutant repeat tracts. In contrast to the chromosomal circularization reported previously in Schizosaccharomyces pombe mutants defective in telomere maintenance, the K. lactis telomere fusions retained their telomeric DNA repeat sequences.