Directional bias during mating type switching in Saccharomyces is independent of chromosomal architecture

Simon, Peter J.; Houston, Peter; Broach, James R.

doi:10.1093/emboj/21.9.2282

Cited by 23 publications

(27 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Determination of the Average Spatial Distance between MAT and HMR-The spatial distance between MATa and HMR has been analyzed in a cells (36). These authors introduced Lac repressor binding sites at the MATa locus and Tet repressor binding sites at the HMR locus in a strain expressing GFP-LacI and GFP-TetR fusion proteins.…”

Section: Resultsmentioning

confidence: 99%

Mapping in Vivo Chromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction

Dekker

2008

Journal of Biological Chemistry

145

122

View full text Add to dashboard Cite

The higher order arrangement of nucleosomes and the level of compaction of the chromatin fiber play important roles in the control of gene expression and other genomic activities. Analysis of chromatin in vitro has suggested that under near physiological conditions chromatin fibers can become highly compact and that the level of compaction can be modulated by histone modifications. However, less is known about the organization of chromatin fibers in living cells. Here, we combine chromosome conformation capture (3C) data with distance measurements and polymer modeling to determine the in vivo mass density of a transcriptionally active 95-kb GC-rich domain on chromosome III of the yeast Saccharomyces cerevisiae. In contrast to previous reports, we find that yeast does not form a compact fiber but that chromatin is extended with a mass per unit length that is consistent with a rather loose arrangement of nucleosomes. Analysis of 3C data from a neighboring AT-rich chromosomal domain indicates that chromatin in this domain is more compact, but that mass density is still well below that of a canonical 30 nm fiber. Our approach should be widely applicable to scale 3C data to real spatial dimensions, which will facilitate the quantification of the effects of chromatin modifications and transcription on chromatin fiber organization.The higher order organization of chromatin is thought to play critical roles in processes such as gene expression. Although the structure of nucleosomes is known in detail, much less is known about higher levels of chromatin organization. The first level of organization beyond the nucleosome may involve formation of a 30-nm-thick chromatin fiber, but the precise organization of DNA within this structure and the range of compaction levels of this fiber are poorly understood (for reviews see, e.g. Refs. 1-9).Over the years, several models have been proposed for the arrangement of nucleosomes within chromatin fibers (reviewed in Refs. 2, 4, 8 -11). Two models have been considered extensively. First, the solenoid model predicts that nucleosomes follow a one-start helical path in which consecutive nucleosomes along the DNA are also nearest neighbors in the fiber (12). Second, the crossed-linker model predicts a threedimensional zigzag organization of nucleosomes that can give rise to a two-start helix (13-15). In this model consecutive nucleosomes are located on opposite sides, with the linker DNA crossing the fiber. This model is supported by in situ observations, nuclease sensitivity experiments, modeling, and crystallographic studies of short tetranucleosomal assemblies (10, 16 -20).Both the solenoid one-step model and the zigzag two-start helix allow formation of chromatin fibers with highly variable levels of chromatin compaction. The level of compaction is thought to affect processes such as transcription. Highly compact chromatin fibers may be less accessible for protein complexes involved in gene expression, DNA repair, and DNA replication. A key step in many chromosomal processes may the...

show abstract

Section: Resultsmentioning

confidence: 99%

Mapping in Vivo Chromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction

Dekker

2008

Journal of Biological Chemistry

145

122

View full text Add to dashboard Cite

show abstract

“…Nonetheless this occurs in HO ϩ yeast cells once per cell cycle with remarkable fidelity. Previous studies have tried without success to identify mating-type-specific spatial clues that predispose one HM locus and not the other to interact with the cleaved MAT locus (4,49). Although neither found matingtype-specific juxtaposition, it was argued that Chr3L has a distinct mobility in MATa versus MAT␣ cells, which might favor exchange with MATa (4).…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, it was proposed that the preference of MATa for HML␣ could be achieved by a cell-type-specific subnuclear juxtaposition of the relevant loci. To test this, Simon et al (49) examined the spatial relationship between the HM loci and MAT by fluorescently tagging pairs of loci in diploid cells in which one allele of the active MAT was deleted. They found that the relative positions of the three mating type loci are identical in MATa and MAT␣ cells.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Regulation of Nuclear Positioning and Dynamics of the Silent Mating Type Loci by the Yeast Ku70/Ku80 Complex

Bystricky

Attikum

Montiel

et al. 2009

Molecular and Cellular Biology

View full text Add to dashboard Cite

We have examined the hypothesis that the highly selective recombination of an active mating type locus (MAT) with either HML␣ or HMRa is facilitated by the spatial positioning of relevant sequences within the budding yeast (Saccharomyces cerevisiae) nucleus. However, both position relative to the nuclear envelope (NE) and the subnuclear mobility of fluorescently tagged MAT, HML, or HMR loci are largely identical in haploid a and ␣ cells. Irrespective of mating type, the expressed MAT locus is highly mobile within the nuclear lumen, while silent loci move less and are found preferentially near the NE. The perinuclear positions of HMR and HML are strongly compromised in strains lacking the Silent information regulator, Sir4. However, HML␣, unlike HMRa and most telomeres, shows increased NE association in a strain lacking yeast Ku70 (yKu70). Intriguingly, we find that the yKu complex is associated with HML and HMR sequences in a mating-typespecific manner. Its abundance decreases at the HML␣ donor locus and increases transiently at MATa following DSB induction. Our data suggest that mating-type-specific binding of yKu to HML␣ creates a local chromatin structure competent for recombination, which cooperates with the recombination enhancer to direct donor choice for gene conversion of the MATa locus.Long-range interactions between two genomic loci in distinct nuclear and chromatin environments are thought to influence recombination and transcription and to contribute to gene control during cell type differentiation in multicellular organisms (1,17,48,50). In Saccharomyces cerevisiae, a-or ␣-cell type is determined by two homeobox-containing genes transcribed at the MAT locus. The ability of yeast cells to switch mating type requires transcriptionally silent copies of both a and ␣ information, which are generally found at the homologous mating type loci HML and HMR (19). Genes at the HM loci, like genes in subtelomeric regions, are prone to position-dependent transcriptional repression. This repression is mediated by the recruitment and spreading of a Silent information regulatory (Sir) complex of Sir2, Sir3, and Sir4 (45).For subtelomeric genes, Sir-mediated repression is facilitated by the clustering of telomeres near the nuclear envelope (NE) (18, 21, 51), which generates a high local concentration of Sir factors. Since Sir factors are limiting for repression (32), the juxtaposition of a reporter gene near such clusters favors repression (2). Telomere anchoring itself is mediated by two redundant pathways: one that requires the yeast Ku70/Ku80 (yKu70/80) complex, and a second that is mediated by Sir4 interaction with the membrane-associated Enhancer of silent chromatin 1 (Esc1) (21, 51). In contrast to the repression that is enhanced by NE association, the interaction of active genes with nuclear pore complexes can increase transcript levels for some inducible genes, possibly by providing a barrier between active and inactive chromatin domains (1,48).In this study, we have examined whether there is cell-typespecifi...

show abstract

“…Donor choice has been studied for mating-type switching in the yeast Saccharomyces cerevisiae where DSBs at MAT initiate conversion that depends on interactions with linked homologous sequences located on opposite arms of the chromosome. Donor choice in this highly specialized system involves a recombination enhancer sequence that regulates recombination across an entire chromosome arm (21), although the physical proximity of donor and recipient loci also plays a role (33,63). A more general case of mitotic DSB-induced gene conversion in yeast was examined by Inbar and Kupiec (25) in which a broken allele could be repaired from either of two ectopic loci on heterologous chromosomes.…”

mentioning

confidence: 99%

Transcription of a Donor Enhances Its Use during Double-Strand Break-Induced Gene Conversion in Human Cells

Schildkraut

Miller

Nickoloff

2006

Molecular and Cellular Biology

View full text Add to dashboard Cite

Homologous recombination (HR) mediates accurate repair of double-strand breaks (DSBs) but carries the risk of large-scale genetic change, including loss of heterozygosity, deletions, inversions, and translocations. Nearly one-third of the human genome consists of repetitive sequences, and DSB repair by HR often requires choices among several homologous repair templates, including homologous chromosomes, sister chromatids, and linked or unlinked repeats. Donor preference during DSB-induced gene conversion was analyzed by using several HR substrates with three copies of neo targeted to a human chromosome. Repair of I-SceI nucleaseinduced DSBs in one neo (the recipient) required a choice between two donor neo genes. When both donors were downstream, there was no significant bias for proximal or distal donors. When donors flanked the recipient, we observed a marked (85%) preference for the downstream donor. Reversing the HR substrate in the chromosome eliminated this preference, indicating that donor choice is influenced by factors extrinsic to the HR substrate. Prior indirect evidence suggested that transcription might increase donor use. We tested this question directly and found that increased transcription of a donor enhances its use during gene conversion. A preference for transcribed donors would minimize the use of nontranscribed (i.e., pseudogene) templates during repair and thus help maintain genome stability.DNA double-strand breaks (DSBs) are potentially lethal events that can be repaired by homologous recombination (HR) or nonhomologous end-joining (NHEJ). If left unrepaired, DSBs can lead to chromosome loss or cell death. DSBs are caused by ionizing radiation, X-rays, free radicals, chemicals, and nucleases and may occur at stalled replication forks (30). Although DSB repair can be accurate, misrepair can have serious consequences. Genomic rearrangements arising during DSB repair can lead to loss of heterozygosity and, ultimately, carcinogenesis through the activation of proto-oncogenes or inactivation of tumor suppressor genes (4, 45). HR appears to be essential for maintaining genome stability. Cells with defects in HR proteins such as BRCA1/2, XRCC2/3, and other RAD51 paralogs exhibit high levels of genomic instability (6,18,28,42,43,52,68). DSBs are a critical type of DNA damage; unlike single-strand breaks, which have a readily available template for repair, DSB repair by HR requires a search for a homologous template.Repetitive elements make up one-third of the mammalian genome and consist of coding DNA, and noncoding DNA such as satellites that can exist in thousands of copies. Repetitive sequences are scattered throughout the genome, including SINE and LINE elements, and ribosomal RNA gene repeats. HR between linked or unlinked repetitive elements can result in a variety of rearrangements including translocations, duplications, and deletions (45).When DNA is broken, there are many potential homologous sequences that could be used as a repair template, including linked or unlinked repeats, sister...

show abstract

Directional bias during mating type switching in Saccharomyces is independent of chromosomal architecture

Cited by 23 publications

References 33 publications

Mapping in Vivo Chromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction

Mapping in Vivo Chromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction

Regulation of Nuclear Positioning and Dynamics of the Silent Mating Type Loci by the Yeast Ku70/Ku80 Complex

Transcription of a Donor Enhances Its Use during Double-Strand Break-Induced Gene Conversion in Human Cells

Contact Info

Product

Resources

About