The Chromatin Remodeler Isw1 Prevents CAG Repeat Expansions During Transcription in<i>Saccharomyces cerevisiae</i>

Koch, Melissa R.; House, Nealia C.M.; Cosetta, Casey M.; Jong, Robyn M.; Salomon, Christelle G; Joyce, Cailin E.; Philips, Elliot A.; Su, Xiaofeng A.; Freudenreich, Catherine H.

doi:10.1534/genetics.117.300529

Cited by 13 publications

(20 citation statements)

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“…Remarkably, TC-NER appears to be responsible for transcription-induced repeat instability in dividing yeast (454,455), human cell cultures (330,456), and mouse neurons (457). The latter might reflect a role for this pathway in somatic expansions of CAG repeats (Fig.…”

Section: Nermentioning

confidence: 95%

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On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

Khristich

Mirkin

2020

Journal of Biological Chemistry

215

239

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Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?

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Section: Nermentioning

confidence: 95%

“…Furthermore, patterns of nucleosome assembly might be an important factor controlling repeat expansion (455,474). The fact that ATTCT (475) and CAG (474,476,477) repeats are potent nucleosome-positioning elements in vitro likely contributes to their instability.…”

Section: Role Of the Chromatin Environment In Repeat Instabilitymentioning

confidence: 99%

On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

Khristich

Mirkin

2020

Journal of Biological Chemistry

215

239

View full text Add to dashboard Cite

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“…Alternatively, addition of a second marker gene to the end of the YAC can be utilized to eliminate events that are not due to end loss from the quantification. YACs have been constructed that contain both a URA3 and HIS3 marker [108] or both URA3 and ADE2 markers [113]. Addition of the ADE2 marker allows a visual analysis of end loss events, which will generate red FOA R colonies on FOA-Leu plates.…”

Section: Genetic Assays To Detect Dna Recombination and Repairmentioning

confidence: 99%

“…Addition of the ADE2 marker allows a visual analysis of end loss events, which will generate red FOA R colonies on FOA-Leu plates. Other derivatives of the YAC have been made that alter the level of transcription through the CAG tract by flanking it with either transcription terminators or addition of a galactose-inducible (pGal) promoter [112, 113].…”

Section: Genetic Assays To Detect Dna Recombination and Repairmentioning

confidence: 99%

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

Klein¹,

Bačinskaja²,

Che³

et al. 2019

Microb Cell

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Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

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“…The DNA was extracted twice using an equal volume of chloroform and finally precipitated by adding 67 µl 7.5M NH4OAc and 500 μl isopropanol. Southern Detection: MNase digested DNA (20-30 μg) was run on 1.5% agarose at 80V for 6hr and then Southern blotted as previously described (62). Chromatin structure was probed with a P 32 labeled 358 bp PCR fragment amplified from 102 bp upstream of the CAG repeat on YAC CF1.…”

Section: Chromatin Analysis By Mnase Digestion and Indirect End-labelmentioning

confidence: 99%

Saccharomyces cerevisiaeH2A copies differentially contribute to recombination and CAG/CTG repeat maintenance, with a role for H2A.1 threonine 126

House

Polleys

Quasem

et al. 2018

Preprint

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DNA are sites of genomic instability. Long CAG/CTG repeats form hairpin structures, are fragile, and can expand during DNA repair. The chromatin response to DNA damage can influence repair fidelity, but the knowledge of chromatin modifications involved in maintaining repair fidelity within repetitive DNA is limited. In a screen for CAG repeat fragility in Saccharomyces cerevisiae, histone 2A copy 1 (H2A.1) was identified to protect the repeat from increased rates of breakage. To address the role of H2A in CAG repeat instability, we tested the effect of deleting each histone H2 subytpe. Whereas deletion of HTA2, HTZ1, HTB1, and HTB2 did not significantly affect CAG repeat maintenance, deletion of HTA1 resulted in increased expansion frequency. Notably, mutation of threonine 126, unique to H2A.1, to a non-phosphorylatable alanine increased CAG repeat instability to a similar level as the hta1Δ mutant. CAG instability in the absence of HTA1 or mutation to hta1-T126A was dependent on the presence of the homologous recombination (HR) repair proteins Rad51, Rad52, and Rad57, and the Polδ subunit Pol32. In addition, sister chromatid recombination (SCR) was suppressed in the hta1Δ and hta1-T126A mutants and this suppression was epistatic to pol32Δ. Finally, break-induced replication (BIR) is impaired in the hta1Δ mutant, resulting in an altered repair profile. These data reveal differential roles for the H2A subtypes in DNA repair and implicate a new role for H2A.1 threonine-126 phosphorylation in mediating fidelity during HR repair and promoting SCR. Using a fragile, repetive DNA element to model endogenous DNA damage, our results demonstrate that H2A.1 plays a greater role than H2A.2 in promoting homology-dependent repair, suggesting H2A.1 is the true homolog of mammalian H2AX, whereas H2A.2 is functionally equivalent to mammalian H2A.Author Summary CAG/CTG trinuncleotide repeats are fragile sequences that when expanded can cause human disease. To evaluate the role of S. cerevisiae histone H2A copies in DNA repair, we have measured instability of an expanded CAG/CTG repeat tract and repair outcomes in H2A mutants. Although the two copies of H2A are nearly identical in amino acid sequence, we found that the CAG repeat is more unstable in the absence of H2A copy 1 (H2A.1) than H2A copy 2, and that this role appears to be partially dependent on a phosphorylatable threonine at residue 126 in the C-terminal tail of H2A.1. Further, we show through a series of genetic assays that H2A.1 plays a role in promoting homologous recombination events, including sister chromatid recombination and break-induced replication. Our results uncover a role for H2A.1 in mediating fidelity of repair within repetitive DNA, and demonstrate that modification of its unique Thr126 residue plays a role in regulating SCR. Given the dependence of HR repair on H2A.1 but not H2A.2, we conclude that H2A.1 plays a greater repair-specific role in the cell and therefore would be the true homolog of mammalian H2AX.

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The Chromatin Remodeler Isw1 Prevents CAG Repeat Expansions During Transcription inSaccharomyces cerevisiae

Abstract: CAG/CTG trinucleotide repeat expansions cause several degenerative neurological and muscular diseases. Koch et al. show that the chromatin remodeling...

Cited by 13 publications

References 82 publications

On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

Saccharomyces cerevisiaeH2A copies differentially contribute to recombination and CAG/CTG repeat maintenance, with a role for H2A.1 threonine 126

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