The Specificity and Topology of Chromatin Interaction Pathways in Yeast

Heterochromatin is a specialized chromatin structure that is central to eukaryotic transcriptional regulation and genome stability. Despite its globally repressive role, heterochromatin must also be dynamic, allowing for its repair and replication. In budding yeast, heterochromatin formation requires silent information regulators (Sirs) Sir2p, Sir3p, and Sir4p, and these Sir proteins create specialized chromatin structures at telomeres and silent mating-type loci. Previously, we found that the SWI/SNF chromatin remodeling enzyme can catalyze the ATP-dependent eviction of Sir3p from recombinant nucleosomal arrays, and this activity enhances early steps of recombinational repair in vitro. Here, we show that the ATPase subunit of SWI/SNF, Swi2p/Snf2p, interacts with the heterochromatin structural protein Sir3p. Two interaction surfaces are defined, including an interaction between the ATPase domain of Swi2p and the nucleosome binding, Bromo-AdjacentHomology domain of Sir3p. A SWI/SNF complex harboring a Swi2p subunit that lacks this Sir3p interaction surface is unable to evict Sir3p from nucleosomes, even though its ATPase and remodeling activities are intact. In addition, we find that the interaction between Swi2p and Sir3p is key for SWI/SNF to promote resistance to replication stress in vivo and for establishment of heterochromatin at telomeres.A ll eukaryotic genomes are stored within the nucleoprotein structure of chromatin, the core subunit of which, the nucleosome, consists of 147 base pairs (bp) of DNA wrapped ∼1.7 times around an octamer of histone proteins (1). Over millions of years, eukaryotes have incorporated chromatin structure into the regulation of many aspects of DNA metabolism, from simple nuclear packaging to transcriptional control (2). This diversity of purpose is reflected in two general types of chromatin structures within the nucleus-euchromatin, which is decondensed and transcriptionally active, and heterochromatin, which is typically localized to the nuclear periphery and repressive for DNA recombination and transcription. Heterochromatin structures are commonly associated with centromeres and telomeres, and these domains package much of a genome's repetitive DNA (3). Consequently, the maintenance of heterochromatin is key for genomic integrity, because it prevents illicit recombination among DNA repeats and promotes chromosome segregation during mitosis (4, 5).On a molecular level, heterochromatic loci are marked by specific chromatin posttranslational modifications, which are recognized and bound by characteristic nonhistone proteins. In many vertebrates, heterochromatin is characterized by members of the heterochromatin protein 1 (HP1) family of proteins, whereas in budding yeast, the silent information regulator (Sir) proteins, Sir2p, Sir3p, and Sir4p, create heterochromatin structures at telomeres and the silent mating-type loci (6, 7). Sir3p is believed to be the key structural component of yeast heterochromatin-Sir3p contains numerous protein-protein interaction motifs (8-10), incl...

show abstract

“…S3 B and C and Dataset S1). Consistent with previous work (27), swi2-Δ10R did not affect SIR2 or SIR3 expression (Fig. S3D and Dataset S1).…”

supporting

confidence: 92%

Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme

Manning

Peterson

2014

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…SET1 Deletion Causes Increased CTD Serine 5 Phosphorylation-Although cells lacking SET1 exhibit changes in the transcription levels of some genes (12,37), they often show alterations in the induction or repression kinetics of regulated genes (13,38,39). Deletion of SET1 also confers sensitivity to the drug 6AU (20), which slows transcription elongation by depleting NTP pools.…”

Section: Resultsmentioning

confidence: 99%

Yeast Swd2 Is Essential Because of Antagonism between Set1 Histone Methyltransferase Complex and APT (Associated with Pta1) Termination Factor

Soares¹,

Buratowski

2012

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

“…S5A) nor does it cause a significant change in the expression levels of other splicing proteins. 71 Utilizing antibodies that recognize either the HA-tag found in the splicing proteins or the Rpb3 subunit of RNA Pol II, we found that deletion of SET2 resulted in a significant decrease in association of Lea1-HA in both the intron regions of the RPS21B and SRB2 genes (p < 0.05) as well as the some of the exon regions of the premRNA (Fig. 6B).…”

Section: Association Ofmentioning

confidence: 92%

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

The Specificity and Topology of Chromatin Interaction Pathways in Yeast

Cited by 221 publications

References 65 publications

Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme

Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme

Yeast Swd2 Is Essential Because of Antagonism between Set1 Histone Methyltransferase Complex and APT (Associated with Pta1) Termination Factor

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

Contact Info

Product

Resources

About