Biology subjects

Usdin, K.

Publications and source records attributed to Usdin, K..

5 recordsLinked to original sources

bioRxiv2024

MSH2 is not required for either maintenance of DNA methylation or repeat contraction at the FMR1 locus in fragile X syndrome

BackgroundRepeat-induced epigenetic changes are observed in many repeat expansion disorders (REDs). These changes result in transcriptional deficits and/or silencing of the associated gene. MSH2, a mismatch repair protein that is required for repeat expansion in the REDs, has been implicated in the maintenance of DNA methylation seen in the region surrounding expanded CTG repeats at the DMPK locus in myotonic dystrophy type 1 (DM1). Here, we investigated the role of MSH2 in aberrant DNA methylation in two additional REDs, fragile X syndrome (FXS) that is caused by a CGG repeat expansion in the 5 untranslated region (UTR) of the fragile X messenger ribonucleoprotein 1 (FMR1) gene, and Friedreichs ataxia (FRDA) that is caused by GAA repeat expansion in intron 1 of the frataxin (FXN) gene. ResultsIn contrast to what is seen at the DMPK locus in DM1, loss of MSH2 did not decrease DNA methylation at the FMR1 promoter in FXS embryonic stem cells (ESCs) or increase FMR1 transcription. This difference was not due to the differences in the CpG density of the two loci as a decrease in DNA methylation was also not observed in a less CpG dense region upstream of the expanded GAA repeats in the FXN gene in MSH2 null induced pluripotent stem cells (iPSCs) derived from FRDA patient fibroblasts. Surprisingly given previous reports, we found that FMR1 reactivation was associated with a high frequency of MSH2- independent repeat contractions that resulted a permanent loss of DNA methylation. ConclusionsOur results suggest that there are mechanistic differences in the way that DNA methylation is maintained in the vicinity of expanded repeats among different REDs even though they share a similar mechanism of repeat expansion. The high frequency of transcription- induced MSH2-independent contractions we have observed may contribute to the mosaicism that is frequently seen in carriers of FMR1 alleles with expanded CGG-repeat tracts. Given the recent interest in the therapeutic use of transcription-driven repeat contractions, our data may have interesting mechanistic, prognostic, and therapeutic implications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/629815v1_ufig1.gif" ALT="Figure 1000"> View larger version (20K): org.highwire.dtl.DTLVardef@1a6a59aorg.highwire.dtl.DTLVardef@1c25fdborg.highwire.dtl.DTLVardef@23394eorg.highwire.dtl.DTLVardef@876445_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Repeat expansion in a Fragile X model is independent of double strand break repair mediated by Pol θ, Rad52, Rad54l or Rad54b

Microsatellite instability is responsible for the human Repeat Expansion Disorders. The mutation responsible differs from classical cancer-associated microsatellite instability (MSI) in that it requires the mismatch repair proteins that normally protect against MSI. LIG4, an enzyme essential for non-homologous end-joining (NHEJ), the major pathway for double-strand break repair (DSBR) in mammalian cells, protects against expansion in mouse models. Thus, NHEJ may compete with the expansion pathway for access to a common intermediate. This raises the possibility that expansion involves an NHEJ-independent form of DSBR. Pol {theta}, a polymerase involved in the theta-mediated end joining (TMEJ) DSBR pathway, has been proposed to play a role in repeat expansion. Here we examine the effect of the loss of Pol {theta} on expansion in FXD mouse embryonic stem cells (mESCs), along with the effects of mutations in Rad52, Rad54l and Rad54b, genes important for multiple DSBR pathways. None of these mutations significantly affected repeat expansion. These observations put major constraints on what pathways are likely to drive expansion. Together with our previous demonstration of the protective effect of nucleases like EXO1 and FAN1, and the importance of Pol {beta}, they suggest a plausible model for late steps in the expansion process.

genetics↗

bioRxiv2024

PMS2 has both pro-mutagenic and anti-mutagenic effects on repeat instability in the Repeat Expansion Diseases

Expansion of a disease-specific tandem repeat is responsible for >45 Repeat Expansion Diseases (REDs). The expansion mutation in each of these diseases has different pathological consequences and most are currently incurable. If the underlying mechanism of mutation is shared, a strategy that slows repeat expansion in one RED may be applicable to multiple REDs. However, the fact that PMS2, a component of the MutL mismatch repair complex, promotes expansion in some models and protects against it in others suggests that the expansion mechanisms may differ. We show here using mouse models of two REDs caused by different repeats that PMS2 has similar effects in both models, with the loss of PMS2 resulting in an increase in expansions in some tissues and a loss of expansion in others. This is consistent with a protective effect of PMS2 in the first case and a role in promoting expansion in the second. Furthermore, we show in mouse embryonic stem cells that lower levels of PMS2 promote expansion while higher levels protect against it, with the ability to promote expansion depending on the PMS2 nuclease domain. Our findings lend support to the hypothesis that REDs share a common expansion mechanism and provide insights into the processes involved. Significance statementCollectively the Repeat Expansion Diseases (REDs) represent a significant health burden. Since the consequences of the expansion mutation differ across diseases, therapeutic approaches that block the underlying mutation are appealing, particularly if the mechanism is shared. However, the conflicting effects of PMS2 loss in different RED models challenges this idea. Here we show using two different RED models that these disparate effects can be reconciled into a single model of repeat expansion, thus increasing confidence that the REDs do all share a common mutational mechanism.

genetics↗

bioRxiv2023

All three MutL complexes are required for repeat expansion in a human stem cell model of CAG-repeat expansion mediated glutaminase deficiency.

The Repeat Expansion Diseases (REDs) arise from the expansion of a disease-specific short tandem repeat (STR). Different REDs differ with respect to the repeat involved, the cells that are most expansion prone and the extent of expansion. Furthermore, whether these diseases share a common expansion mechanism is unclear. To date, expansion has only been studied in a limited number of REDs. Here we report the first studies of the expansion mechanism in induced pluripotent stem cells derived from a patient with a form of the glutaminase deficiency disorder known as Global Developmental Delay, Progressive Ataxia, And Elevated Glutamine (GDPAG; OMIM# 618412) caused by the expansion of a CAG-STR in the 5 UTR of the glutaminase (GLS) gene. We show that alleles with as few as [~]120 repeats show detectable expansions in culture despite relatively low levels of R-loops formed at this locus. Additionally, using a CRISPR-Cas9 knockout approach we show that PMS2 and MLH3, the constituents of MutL and MutL{gamma}, the 2 mammalian MutL complexes known to be involved in mismatch repair (MMR), are essential for expansion. Furthermore, PMS1, a component of a less well understood MutL complex, MutL{beta}, is also important, if not essential, for repeat expansion in these cells. Our results provide insights into the factors important for expansion and lend weight to the idea that, despite some differences, the same mechanism is responsible for expansion in many, if not all, REDs.

genetics↗

bioRxiv2022

Linking Dynamic DNA Secondary Structures to Genome Instability

Genomic double-stranded DNA (dsDNA) becomes single-stranded (ssDNA) during replication, transcription, and DNA repair. ssDNA is therefore believed to be transient, occurring in only a fraction of the genome at a given time, and variable amongst a population of cells. These transiently formed ssDNA segments can also adopt alternative, dynamic DNA conformations, such as cruciform DNA, triplexes, quadruplexes and others. To determine whether there are stable and conserved regions of ssDNA, we utilized our previously developed method S1-END-seq 1 to convert ssDNA to DNA double strand breaks (DSBs), which are then processed for high-throughput sequencing. This approach revealed two predominant dynamic DNA structures: cruciform DNA formed by expanded (TA)n repeats that accumulated uniquely in microsatellite unstable human cancer cell lines, and DNA triplexes (H-DNA) formed by homopurine/homopyrimidine (hPu/hPy) mirror repeats common across a variety of human cell lines. Triplex-forming repeats accumulated during replication, blocked DNA synthesis and were hotspots of somatic mutation. In contrast, pathologically expanded (hPu/hPy) repeats in Friedreichs ataxia patient cells formed a replication-independent and transcription-inducible DNA secondary structure. Our results identify dynamic DNA secondary structures in vivo that contribute to elevated genome instability.

molecular biology↗