A Role for Chd1 and Set2 in Negatively Regulating DNA Replication in <i>Saccharomyces cerevisiae</i>

Biswas, Debabrata; Takahata, Shinya; Hua, Xin; Dutta-Biswas, Rinku; Yu, Yan; Formosa, Tim; Stillman, David J.

doi:10.1534/genetics.107.084202

Cited by 46 publications

(42 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The FACT complex plays an important role in DNA replication (6,54,57,58), and our results suggest that the NuA4 KAT complex is also involved in DNA replication. A mutation in the Esa1 catalytic subunit results in mild sensitivity to HU, and an spt16 esa1 double mutant shows additivity in HU sensitivity.…”

Section: Discussionsupporting

confidence: 56%

Different Genetic Functions for the Rpd3(L) and Rpd3(S) Complexes Suggest Competition between NuA4 and Rpd3(S)

Biswas

Takahata

Stillman

2008

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

Rpd3(L) and Rpd3(S) are distinct multisubunit complexes containing the Rpd3 histone deacetylase. Disruption of the GCN5 histone acetyltransferase gene shows a strong synthetic phenotype when combined with either an sds3 mutation affecting only the Rpd3(L) complex or an rco1 mutation affecting only Rpd3(S). However, these synthetic growth defects are not seen in a gcn5 sds3 rco1 triple mutant, suggesting that the balance between Rpd3(L) and Rpd3(S) is critical in cells lacking Gcn5. Different genetic interactions are seen with mutations affecting the FACT chromatin reorganizing complex. An sds3 mutation affecting only Rpd3(L) has a synthetic defect with FACT mutants, while rco1 and eaf3 mutations affecting Rpd3(S) suppress FACT mutant phenotypes. Rpd3(L) therefore acts in concert with FACT, but Rpd3(S) opposes it. Combining FACT mutations with mutations in the Esa1 subunit of the NuA4 histone acetyltransferase results in synthetic growth defects, and these can be suppressed by an rco1 or set2 mutation. An rco1 mutation suppresses phenotypes caused by mutations in the ESA1 and ARP4 subunits of NuA4, while Rco1 overexpression exacerbates these defects. These results suggest a model in which NuA4 and Rpd3(S) compete. Chromatin immunoprecipitation experiments show that eliminating Rpd3(S) increases the amount of NuA4 binding to the ARG3 promoter during transcriptional activation and to the sites of DNA repair induced by a double-strand break. Our results suggest that the Rpd3(L) and Rpd3(S) complexes have distinct functions in vivo and that the relative amounts of the two forms alter the effectiveness of other chromatin-altering complexes, such as FACT and NuA4.

show abstract

Section: Discussionsupporting

confidence: 56%

Different Genetic Functions for the Rpd3(L) and Rpd3(S) Complexes Suggest Competition between NuA4 and Rpd3(S)

Biswas

Takahata

Stillman

2008

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

show abstract

“…5C and 5D), indicative of a transcription elongation defect. We and others have shown that set2D bypasses the slow growth phenotype of spt16-11 at semi-permissive temperature (of 35 C) 68,69 and that set2D is resistant to 6-AU. 36 Since FACT is a positive regulator of transcription elongation, and 6-AU results in elongation defects, bypass of spt16-11 mutant and resistance to 6-AU suggests Set2 as a negative regulator of transcription elongation.…”

Section: Association Ofmentioning

confidence: 74%

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

et al. 2016

View full text Add to dashboard Cite

Co-transcriptional splicing takes place in the context of a highly dynamic chromatin architecture, yet the role of chromatin restructuring in coordinating transcription with RNA splicing has not been fully resolved. To further define the contribution of histone modifications to pre-mRNA splicing in Saccharomyces cerevisiae, we probed a library of histone point mutants using a reporter to monitor pre-mRNA splicing. We found that mutation of H3 lysine 36 (H3K36) -a residue methylated by Set2 during transcription elongation -exhibited phenotypes similar to those of pre-mRNA splicing mutants. We identified genetic interactions between genes encoding RNA splicing factors and genes encoding the H3K36 methyltransferase Set2 and the demethylase Jhd1 as well as point mutations of H3K36 that block methylation. Consistent with the genetic interactions, deletion of SET2, mutations modifying the catalytic activity of Set2 or H3K36 point mutations significantly altered expression of our reporter and reduced splicing of endogenous introns. These effects were dependent on the association of Set2 with RNA polymerase II and H3K36 dimethylation. Additionally, we found that deletion of SET2 reduces the association of the U2 and U5 snRNPs with chromatin. Thus, our study provides the first evidence that H3K36 methylation plays a role in co-transcriptional RNA splicing in yeast.Abbreviations: (H3K36), histone H3 lysine 36; (ChIP), chromatin immunoprecipitations; (RT-qPCR), reverse transcription PCR; (snRNP), small nuclear ribonucleprotein; (RNA Pol II), RNA polymerase II

show abstract

“…At least some FACT mutants retain normal induction of RNR gene transcription (Biswas et al 2008;Formosa 2008), so HU sensitivity often reflects a defect in DNA replication, but indirect effects due to flawed transcription are also possible. The Spt 2 phenotype results from inappropriate transcription initiation start-site selection (Clark-Adams et al 1988), indicating that spt16-11 causes a defect in transcription even at temperatures permissive for growth where Spt16 protein levels are normal.…”

Section: Resultsmentioning

confidence: 99%

“…Some features of chromatin therefore support FACT activity in vivo, and their loss makes FACT defects more difficult to tolerate. In contrast, other chromatin factors oppose FACT activity, as the phenotypes caused by some FACT gene mutations can be suppressed by preventing methylation of H3-K36 (Biswas et al 2006) or by inactivating the chromodomain-helicase Chd1 (Biswas et al 2008). FACT gene mutations can also either enhance or suppress defects caused by mutating other chromatin factors such as the histone H3 or the Swi/Snf remodeling complex (Malone et al 1991;Duina et al 2007).…”

mentioning

confidence: 99%

Insight Into the Mechanism of Nucleosome Reorganization From Histone Mutants That Suppress Defects in the FACT Histone Chaperone

et al. 2011

Self Cite

View full text Add to dashboard Cite

FACT (FAcilitates Chromatin Transcription/Transactions) plays a central role in transcription and replication in eukaryotes by both establishing and overcoming the repressive properties of chromatin. FACT promotes these opposing goals by interconverting nucleosomes between the canonical form and a more open reorganized form. In the forward direction, reorganization destabilizes nucleosomes, while the reverse reaction promotes nucleosome assembly. Nucleosome destabilization involves disrupting contacts among histone H2A-H2B dimers, (H3-H4) 2 tetramers, and DNA. Here we show that mutations that weaken the dimer:tetramer interface in nucleosomes suppress defects caused by FACT deficiency in vivo in the yeast Saccharomyces cerevisiae. Mutating the gene that encodes the Spt16 subunit of FACT causes phenotypes associated with defects in transcription and replication, and we identify histone mutants that selectively suppress those associated with replication. Analysis of purified components suggests that the defective version of FACT is unable to maintain the reorganized nucleosome state efficiently, whereas nucleosomes with mutant histones are reorganized more easily than normal. The genetic suppression observed when the FACT defect is combined with the histone defect therefore reveals the importance of the dynamic reorganization of contacts within nucleosomes to the function of FACT in vivo, especially to FACT's apparent role in promoting progression of DNA replication complexes. We also show that an H2B mutation causes different phenotypes, depending on which of the two similar genes that encode this protein are altered, revealing unexpected functional differences between these duplicated genes and calling into question the practice of examining the effects of histone mutants by expressing them from a single plasmid-borne allele.

show abstract

A Role for Chd1 and Set2 in Negatively Regulating DNA Replication in Saccharomyces cerevisiae

Cited by 46 publications

References 77 publications

Different Genetic Functions for the Rpd3(L) and Rpd3(S) Complexes Suggest Competition between NuA4 and Rpd3(S)

Different Genetic Functions for the Rpd3(L) and Rpd3(S) Complexes Suggest Competition between NuA4 and Rpd3(S)

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

Insight Into the Mechanism of Nucleosome Reorganization From Histone Mutants That Suppress Defects in the FACT Histone Chaperone

Contact Info

Product

Resources

About