Collisions between yeast chromosomal loci in vivo are governed by three layers of organization

Abstract

The relative probabilities that different pairs of chromosomal loci will collide with one another in vegetatively growing diploid yeast cells have been assessed using a genetic assay for Cre/loxP site-specific recombination. Recombination rates have been determined for 18 different pairs of loxP sites representing diverse pairs of positions within the genome. Overall, relative collision probabilities vary over an eightfold range. Within this range, a hierarchy comprising three levels of organization can be discerned. First, collisions between loci on nonhomologous chromosomes are governed by nonspecific centromere clustering. Second, a sequence is closer to allelic or nearby sequences on its homolog than to sequences on nonhomologous chromosomes, an effect most simply attributed to homolog pairing. Third, a sequence can be closer to other sequences nearby on the same chromosome than to sequences on other chromosomes. These findings provide a framework for assessing the role of chromosome disposition in cellular processes such as DNA repair and gene expression. Also the possibility is raised that genome-wide coalignment of homologs is not the fundamental raison d'etre of the somatic pairing process. We suggest instead that pairing may exist to promote juxtaposition of homologous regions within irregular genome complements. Chromosome organization, disposition, and behavior have been investigated by many experimental approaches. A handful of studies have used site-specific recombination reactions to probe chromosome status in living cells. In bacteria, the phage Int reaction has been used to assess in vivo supercoiling levels (Bliska and Cozzarelli 1987); the bacteriophage P1 Cre/loxP recombination reaction has been used to assess effective DNA concentration (Hildebrandt and Cozzarelli 1995); and the ␥-␦ resolvase reaction has been used to probe for domainal organization of chromosomes (e.g., Staczek and Higgins 1998). Also, in Drosophila, the yeast Flp/frt recombination reaction has been used to assess the effect of chromosomal inversions on pairing of allelic regions lying distal to the rearrangement breakpoints (Golic and Golic 1996b) and to compare intrachromosomal versus interchromosomal recombination rates (Golic and Golic 1996a).The current study exploits Cre/loxP site-specific recombination to examine chromosome status in vegetatively growing diploid budding yeast cells. A genetic assay for Cre/loxP recombination in yeast has been developed and used to determine in vivo recombination rates for 18 different pairs of loxP inserts representing various pairs of positions within the genome. The goal of this study was to assess the relative probabilities with which different regions of the genome collide with one another. Cre/loxP recombination seemed to be an appropriate tool for such analysis because the amount of product formed depends on the square of the loxP concentration in vitro and retains its dependence on loxP concentration in vivo in Escherichia coli (Hildebrandt and Cozzarelli 1995). Thus, the relat...

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“…The genome of budding yeast Saccharomyces cerevisiae presents a Rabl organization driven by (i) centromeres clustering at the spindle pole body (SPB, S. cerevisiae microtubule organizing center), (ii) telomeres tethering to the nuclear envelope, (iii) the nucleolus where the rDNA is sequestered opposite to the SPB, and (iv) chromosome arm length (Burgess & Kleckner, 1999; Taddei & Gasser, 2012). Hi‐C experiments have confirmed this Rabl organization, but the existence of sub‐megabase structures within yeast chromosomes similar to mammalian topological associated domains or their bacterial equivalent is still controversial (Duan et al , 2010; Hsieh et al , 2015; Eser et al , 2017).…”

Keep moving and stay in a good shape to find your homologous recombination partner

“…Indeed, several studies in yeast recently showed that recombination efficiency decreases with the spatial distance between a DSB and its homologous targets (Burgess and Kleckner 1999;Agmon et al 2013;Lee et al 2016;Batté et al 2017). Accordingly, sequences actively brought into close proximity either using the MAT Recombination Enhancer (Li et al 2012;Mehta et al 2017) or clustering subtelomeric sequences (Batté et al 2017) recombine more efficiently.…”