scholarly journals Yeast Recombination Enhancer Is Stimulated by Transcription Activation

2005 ◽  
Vol 25 (18) ◽  
pp. 7976-7987 ◽  
Author(s):  
Sevinc Ercan ◽  
Joseph C. Reese ◽  
Jerry L. Workman ◽  
Robert T. Simpson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Noncoding Rnas ◽  
Transcription Activation ◽  
Open Chromatin ◽  
Conserved Domains ◽  
Mating Type Switching ◽  
Chromosome Iii ◽  
Donor Preference ◽  
Recombination Enhancer

ABSTRACT Saccharomyces cerevisiae mating type switching is a gene conversion event that exhibits donor preference. MAT a cells choose HMLα for recombination, and MATα cells choose HMR a. Donor preference is controlled by the recombination enhancer (RE), located between HMLα and MAT a on the left arm of chromosome III. A number of a-cell specific noncoding RNAs are transcribed from the RE locus. Mcm1 and Fkh1 regulate RE activity in a cells. Here we show that Mcm1 binding is required for both the transcription of the noncoding RNAs and Fkh1 binding. This requirement can be bypassed by inserting another promoter into the RE. Moreover, the insertion of this promoter increases donor preference and opens the chromatin structure around the conserved domains of RE. Additionally, we determined that the level of Fkh1 binding positively correlates with the level of donor preference. We conclude that the role of Mcm1 in RE is to open chromatin around the conserved domains and activate transcription; this facilitates Fkh1 binding and the level of this binding determines the level of donor preference.

scholarly journals A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure

2019 ◽  
Author(s):  
Mingguang Li ◽  
Ryan D. Fine ◽  
Manikarna Dinda ◽  
Stefan Bekiranov ◽  
Jeffrey S. Smith
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Control Region ◽  
Mating Type ◽  
Locus Control Region ◽  
A Cells ◽  
Mating Type Switching ◽  
Chromosome Iii ◽  
The Right ◽  
Donor Preference ◽  
Recombination Enhancer

AbstractThe NAD+-dependent histone deacetylase Sir2 was originally identified in Saccharomyces cerevisiae as a silencing factor for HML and HMR, the heterochromatic cassettes utilized as donor templates during mating-type switching. MATa cells preferentially switch to MATα using HML as the donor, which is driven by an adjacent cis-acting element called the recombination enhancer (RE). In this study we demonstrate that Sir2 and the condensin complex are recruited to the RE exclusively in MATa cells, specifically to the promoter of a small gene within the right half of the RE known as RDT1. We go on to demonstrate that the RDT1 promoter functions as a locus control region (LCR) that regulates both transcription and long-range chromatin interactions. Sir2 represses the transcription of RDT1 until it is redistributed to a dsDNA break at the MAT locus induced by the HO endonuclease during mating-type switching. Condensin is also recruited to the RDT1 promoter and is displaced upon HO induction, but does not significantly repress RDT1 transcription. Instead condensin appears to promote mating-type switching efficiency and donor preference by maintaining proper chromosome III architecture, which is defined by the interaction of HML with the right arm of chromosome III, including MATa and HMR. Remarkably, eliminating Sir2 and condensin recruitment to the RDT1 promoter disrupts this structure and reveals an aberrant interaction between MATa and HMR, consistent with the partially defective donor preference for this mutant. Global condensin subunit depletion also impairs mating type switching efficiency and donor preference, suggesting that modulation of chromosome architecture plays a significant role in controlling mating type switching, thus providing a novel model for dissecting condensin function in vivo.Author summarySir2 is a highly conserved NAD+-dependent protein deacetylase and defining member of the sirtuin protein family. It was identified about 40 years ago in the budding yeast, Saccharomyces cerevisiae, as a gene required for silencing of the cryptic mating-type loci, HML and HMR. These heterochromatic cassettes are utilized as templates for mating-type switching, whereby a programmed DNA double-strand break at the MATa or MATα locus is repaired by gene conversion to the opposite mating type. The preference for switching to the opposite mating type is called donor preference, and in MATa cells, is driven by a cis-acting DNA element called the recombination enhancer (RE). It was believed that the only role for Sir2 in mating-type switching was silencing HML and HMR. However, in this study we show that Sir2 also regulates expression of a small gene (RDT1) in the RE that is activated during mating-type switching. The promoter of this gene is also bound by the condensin complex, and deleting this region of the RE drastically changes chromosome III structure and alters donor preference. The RE therefore appears to function as a complex locus control region (LCR) that links transcriptional control to chromatin architecture, and thus provides a new model for investigating the underlying mechanistic principles of programmed chromosome architectural dynamics.

scholarly journals Mechanism of MAT alpha donor preference during mating-type switching of Saccharomyces cerevisiae.

1996 ◽  
Vol 16 (2) ◽  
pp. 657-668 ◽  
Author(s):  
X Wu ◽  
J K Moore ◽  
J E Haber
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Strand Break ◽  
Normal Donor ◽  
Alpha Cells ◽  
Cis Acting ◽  
Mating Type Switching ◽  
Chromosome Iii ◽  
The Right ◽  
Donor Preference

During homothallic switching of the mating-type (MAT) gene in Saccharomyces cerevisiae, a- or alpha-specific sequences are replaced by opposite mating-type sequences copied from one of two silent donor loci, HML alpha or HMRa. The two donors lie at opposite ends of chromosome III, approximately 190 and 90 kb, respectively, from MAT. MAT alpha cells preferentially recombine with HMR, while MATa cells select HML. The mechanisms of donor selection are different for the two mating types. MATa cells, deleted for the preferred HML gene, efficiently use HMR as a donor. However, in MAT alpha cells, HML is not an efficient donor when HMR is deleted; consequently, approximately one-third of HO HML alpha MAT alpha hmr delta cells die because they fail to repair the HO endonuclease-induced double-strand break at MAT. MAT alpha donor preference depends not on the sequence differences between HML and HMR or their surrounding regions but on their chromosomal locations. Cloned HMR donors placed at three other locations to the left of MAT, on either side of the centromere, all fail to act as efficient donors. When the donor is placed 37 kb to the left of MAT, its proximity overcomes normal donor preference, but this position is again inefficiently used when additional DNA is inserted in between the donor and MAT to increase the distance to 62 kb. Donors placed to the right of MAT are efficiently recruited, and in fact a donor situated 16 kb proximal to HMR is used in preference to HMR. The cis-acting chromosomal determinants of MAT alpha preference are not influenced by the chromosomal orientation of MAT or by sequences as far as 6 kb from HMR. These data argue that there is an alpha-specific mechanism to inhibit the use of donors to the left of MAT alpha, causing the cell to recombine most often with donors to the right of MAT alpha.

Homothallic mating type switching generates lethal chromosome breaks in rad52 strains of Saccharomyces cerevisiae

1981 ◽  
Vol 1 (6) ◽  
pp. 522-534
Author(s):  
B Weiffenbach ◽  
J E Haber
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Deoxyribonucleic Acid ◽  
Type Locus ◽  
Mating Type Switching ◽  
Lethal Event ◽  
Bona Fide ◽  
Chromosome Iii ◽  
Mat Locus ◽  
Type Information

In homothallic cells of Saccharomyces cerevisiae, a or alpha mating type information at the mating type locus (MAT) is replaced by the transposition of the opposite mating type allele from HML alpha or HMRa. The rad52-1 mutation, which reduces mitotic and abolishes meiotic recombination, also affects homothallic switching (Malone and Esposito, Proc. Natl. Acad. Sci. U.S.A. 77:503-507, 1980). We have found that both HO rad52 MATa and HO rad52 MAT alpha cells die. This lethality is suppressed by mutations that substantially reduce but do not eliminate homothallic conversions. These mutations map at or near the MAT locus (MAT alpha inc, MATa-inc, MATa stk1) or are unlinked to MAT (HO-1 and swi1). These results suggest that the switching event itself is involved in the lethality. With the exception of swi1, HO rad52 strains carrying one of the above mutations cannot convert mating type at all. MAT alpha rad52 HO swi1 strains apparently can switch MAT alpha to MATa. However, when we analyzed these a maters, we found that few, if any, of them were bona fide MATa cells. These a-like cells were instead either deleted for part of chromosome III distal to and including MAT or had lost the entire third chromosome. Approximately 30% of the time, an a-like cell could be repaired to a normal MATa genotype if the cell was mated to a RAD52 MAT alpha-inc strain. The effects of rad52 were also studied in mata/MAT alpha-inc rad52/rad52 ho/HO diploids. When this diploid attempted to switch mata to MATa, an unstable broken chromosome was generated in nearly every cell. These studies suggest that homothallic switching involves the formation of a double-stranded deoxyribonucleic acid break or a structure which is labile in rad52 cells and results in a broken chromosome. We propose that the production of a double-stranded deoxyribonucleic acid break is the lethal event in rad52 HO cells.

scholarly journals Homothallic mating type switching generates lethal chromosome breaks in rad52 strains of Saccharomyces cerevisiae.

1981 ◽  
Vol 1 (6) ◽  
pp. 522-534 ◽  
Author(s):  
B Weiffenbach ◽  
J E Haber
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Deoxyribonucleic Acid ◽  
Type Locus ◽  
Mating Type Switching ◽  
Lethal Event ◽  
Bona Fide ◽  
Chromosome Iii ◽  
Mat Locus ◽  
Type Information

In homothallic cells of Saccharomyces cerevisiae, a or alpha mating type information at the mating type locus (MAT) is replaced by the transposition of the opposite mating type allele from HML alpha or HMRa. The rad52-1 mutation, which reduces mitotic and abolishes meiotic recombination, also affects homothallic switching (Malone and Esposito, Proc. Natl. Acad. Sci. U.S.A. 77:503-507, 1980). We have found that both HO rad52 MATa and HO rad52 MAT alpha cells die. This lethality is suppressed by mutations that substantially reduce but do not eliminate homothallic conversions. These mutations map at or near the MAT locus (MAT alpha inc, MATa-inc, MATa stk1) or are unlinked to MAT (HO-1 and swi1). These results suggest that the switching event itself is involved in the lethality. With the exception of swi1, HO rad52 strains carrying one of the above mutations cannot convert mating type at all. MAT alpha rad52 HO swi1 strains apparently can switch MAT alpha to MATa. However, when we analyzed these a maters, we found that few, if any, of them were bona fide MATa cells. These a-like cells were instead either deleted for part of chromosome III distal to and including MAT or had lost the entire third chromosome. Approximately 30% of the time, an a-like cell could be repaired to a normal MATa genotype if the cell was mated to a RAD52 MAT alpha-inc strain. The effects of rad52 were also studied in mata/MAT alpha-inc rad52/rad52 ho/HO diploids. When this diploid attempted to switch mata to MATa, an unstable broken chromosome was generated in nearly every cell. These studies suggest that homothallic switching involves the formation of a double-stranded deoxyribonucleic acid break or a structure which is labile in rad52 cells and results in a broken chromosome. We propose that the production of a double-stranded deoxyribonucleic acid break is the lethal event in rad52 HO cells.

scholarly journals A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure

PLoS Genetics ◽  
2019 ◽  
Vol 15 (8) ◽  
pp. e1008339 ◽  
Author(s):  
Mingguang Li ◽  
Ryan D. Fine ◽  
Manikarna Dinda ◽  
Stefan Bekiranov ◽  
Jeffrey S. Smith
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Control Region ◽  
Locus Control Region ◽  
Chromosome Iii ◽  
Recombination Enhancer

scholarly journals Detection of the DNA primary structure modifications induced by the base analog 6-n-hydroxylaminopurine in the alpha-test in yeast saccharomyces cerevisiae

2020 ◽  
Vol 18 (3) ◽  
pp. 357-366
Author(s):  
Anna S. Zhuk ◽  
Elena I. Stepchenkova ◽  
Sergey G. Inge-Vechtomov
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Dna Lesions ◽  
Genetic Toxicology ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genetic Changes ◽  
Mating Type Switching ◽  
Base Modifications ◽  
Type Switch ◽  
Chromosome Iii

Background. The alpha-test allows to detect inherited genetic changes of different types, as well as phenotypic expression of primary DNA lesions before the lesions are fixed by repair. Here we investigate ability of the alpha-test to detect base modifications induced by 6-N-hydroxylaminopurine (HAP) and determine frequency of inherited and non-inherited genetic changes in yeast strains treated with HAP. Materials and methods. The alpha-test is based on mating type regulation and detects cell type switch from to a in heterothallic yeast Saccharomyces cerevisiae. The frequency of mating type switching reflects level of both spontaneous and induced by a mutagen DNA instability. The alpha-test may be performed in two variants: illegitimate hybridization and cytoduction. Conducting both complementary tests and analysis of phenotypes of the illegitimate hybrids and cytoductants allows to detect the full spectrum of genetic events that lead to mating type switching, such as chromosome III loss and chromosome III arm loss, mutations and temporary lesions, recombination and conversion. Results. HAP increases the frequency of illegitimate hybridization by 5-fold, and illegitimate cytoduction by 10-fold. A large proportion of the primary lesions induced by HAP causes temporary mating type switch and the remainder parts are converted into inherited point mutations. Conclusion. The alpha-test can detect HAP-induced base modifications and may be used to investigate the ratio between correct and error-prone processing of such primary DNA lesions. Like other genetic toxicology tests the alpha-test has limitations, which are discussed.

Efficient production of a ring derivative of chromosome III by the mating-type switching mechanism in Saccharomyces cerevisiae

1983 ◽  
Vol 3 (5) ◽  
pp. 803-810
Author(s):  
A J Klar ◽  
J N Strathern ◽  
J B Hicks ◽  
D Prudente
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Genetic Information ◽  
Recombination Event ◽  
Ring Chromosome ◽  
Efficient Production ◽  
Yeast Saccharomyces Cerevisiae ◽  
Type Locus ◽  
Mating Type Switching ◽  
Chromosome Iii

The mating-type switches in the yeast Saccharomyces cerevisiae occur by unidirectional transposition of replicas of unexpressed genetic information, residing at HML or HMR, into the mating-type locus (MAT). The source loci, HML and HMR, remain unchanged. Interestingly, when the HM cassettes are expressed, as in marl strains, the HML and HMR cassettes can also efficiently switch, apparently by obtaining genetic information from either of the other two cassettes (Klar et al., Cell 25:517-524, 1981). We have isolated a novel chromosome III rearrangement in heterothallic (marl ho) strains, which is also produced efficiently in marl HO cells, presumably the consequence of a recombination event between HML and HMR. The fusion results in the loss of sequences which are located distal to HML and to HMR and produces a ring derivative of chromosome III. Cells containing such a ring chromosome are viable as haploids; apparently, no essential loci are located distal to the HM loci. The fusion cassette behaves as a standard HM locus with respect to both regulation by the MAR/SIR control and its role in switching MAT.

scholarly journals The DNA Repair Protein yKu80 Regulates the Function of Recombination Enhancer during Yeast Mating Type Switching

2005 ◽  
Vol 25 (19) ◽  
pp. 8476-8485 ◽  
Author(s):  
Chun Ruan ◽  
Jerry L. Workman ◽  
Robert T. Simpson
Keyword(s):  
Mating Type ◽  
Affinity Purification ◽  
Yeast Mating ◽  
Directional Movement ◽  
Repair Protein ◽  
Dna Repair Protein ◽  
Mating Type Switching ◽  
Donor Preference ◽  
Recombination Enhancer

ABSTRACT Recombination enhancer (RE) is essential for regulating donor preference during yeast mating type switching. In this study, by using minichromosome affinity purification (MAP) and mass spectrometry, we found that yeast Ku80p is associated with RE in MAT a cells. Chromatin immunoprecipitation assays confirmed its occupancy in vivo. Deletion of YKU80 results in altered chromatin structure in the RE region and more importantly causes a dramatic decrease of HML usage in MAT a cells. We also detect directional movement of yKu80p from the RE towards HML during switching. These results indicate a novel function of yeast Ku80p in regulating mating type switching.

scholarly journals Global Chromatin Structure of 45,000 Base Pairs of Chromosome III in a- and α-Cell Yeast and during Mating-Type Switching

2004 ◽  
Vol 24 (22) ◽  
pp. 10026-10035 ◽  
Author(s):  
Sevinc Ercan ◽  
Robert T. Simpson
Keyword(s):  
Mating Type ◽  
Chromatin Structure ◽  
Cell Types ◽  
Open Reading Frames ◽  
Base Pairs ◽  
Distinctive Features ◽  
Hypersensitive Sites ◽  
Mating Type Switching ◽  
Chromosome Iii ◽  
Recombination Enhancer

ABSTRACT Directionality of yeast mating-type switching has been attributed to differences in chromatin structure for the left arm of chromosome III. We have mapped the structure of ∼45 kbp of the left arm of chromosome III in a and α cells in logarithmically growing cultures and in a cells during switching. Distinctive features of chromatin structure were the occurrence of DNase I-hypersensitive sites in the promoter region of nearly every gene and some replication origins and the presence of extended regions of positioned nucleosomes in ∼25% of the open reading frames. Other than the recombination enhancer, chromatin structures were identical in the two cell types. Changes in chromatin structure during switching were confined to the recombination enhancer. This unbiased analysis of an extended region of chromatin reveals that significant features of organized chromatin exist for the entire region, and these features are largely static with respect to mating type and mating-type switching. Our analysis also shows that primary chromatin structure does not cause the documented differences in recombinational frequency of the left arm of chromosome III in yeast a and α cells.

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