WDR5, BRCA1, and BARD1 Co-regulate the DNA Damage Response and Modulate the Mesenchymal-to-Epithelial Transition during Early Reprogramming

Peñalosa-Ruiz, Georgina; Bousgouni, Vicky; Gerlach, Jan P.; Waarlo, Susan; Ven, Joris V. van de; Veenstra, Tim; Silva, José C.R.; Heeringen, Simon J. van; Bakal, Chris; Mulder, Klaas W.; Veenstra, G.J.C.

doi:10.1016/j.stemcr.2019.02.006

Cited by 20 publications

(42 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is well known that WDR5 forms the histone H3 lysine 4 methyltransferase complex with mixed lineage leukaemia (MLL, MLL1-4) and promotes RNA polymerase II-dependent transcription activation (40). In addition, it was recently suggested that WDR5, BRCA1 and BRAD1 were functionally connected to suppress DNA damage during reprogramming (41). ZMYND8 was reported to play roles in activating transcription and promoting HR via multivalent binding to chromatin, including histone H4 acetlylations (30,42,43).…”

Section: Discussionmentioning

confidence: 99%

A novel nuclear speckle factor, USP42, promotes homologous recombination repair by resolving DNA double-strand break induced R-loop

Matsui

Sakasai

Abe

et al. 2019

Preprint

View full text Add to dashboard Cite

The nucleus of mammalian cells is highly compartmentalized by nuclear bodies, including nuclear speckles. While nuclear bodies are known to function in regulating gene expression, their involvement in DNA repair has not been actively investigated. Here, our focused screen for nuclear speckle factors involved in homologous recombination (HR), which is a faithful DNA double-strand break (DSB) repair mechanism, revealed that nuclear speckle factors regulating transcription are potentially involved in the regulation of HR. Among the top hits, we provide evidence showing that USP42, which is a deubiquitylating enzyme and a hitherto unidentified nuclear speckles factor, promotes HR by facilitating BRCA1 recruitment to DSB sites and DNA-end resection. We further showed that USP42 localizes to nuclear speckles via an intrinsically disordered region, which is required for efficient HR. Furthermore, we established that USP42 interacts with DHX9, which possesses DNA-RNA helicase activity, and is required for efficient resolution of DSB-induced R-loop. Mechanistically, USP42antagonizes mono-ubiquitylation of DHX9 that is evoked after DSB induction. In conclusion, our data propose a model in which a novel nuclear speckle factor, USP42, facilitates DSBinduced R-loop resolution, BRCA1 loading to DSB sites and preferential DSB repair by HR, indicating the importance of spatial regulation of DSB repair choice mediated by nuclear bodies. KeywordsNuclear speckles, DNA double-strand break, homologous recombination, USP42, DHX9, Rloop, ubiquitylation, deubiquitylation Significant statementDefects in the repair of DNA double-strand break (DSB), which is one of the most harmful DNA insults, cause human diseases including cancers. It has been suggested that DSBs generated in the coding region tend to be repaired by homologous recombination (HR) that is error-free DSB repair pathway. To reveal the spatial regulation of HR, in this study, we investigated the potential contribution of nuclear bodies, especially nuclear speckles, to HR, identifying a deubiquitylating enzyme USP42 as a HR promoting factor. We found that USP42 deubiquitylates DHX9, facilitates resolution of DNA-RNA hybrid structure and enhances HR through BRCA1 loading to DSB sites.

show abstract

Section: Discussionmentioning

confidence: 99%

A novel nuclear speckle factor, USP42, promotes homologous recombination repair by resolving DNA double-strand break induced R-loop

Matsui

Sakasai

Abe

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…In a previous study, we performed a high-content siRNA screen, targeting 300 chromatin-associated factors during early reprogramming ( Fig. 1A) [23]. We hypothesized that the onset of reprogramming would be associated with colonylevel phenotypic changes and that these changes are affected upon gene perturbation.…”

Section: High Content Screening Reveals Early Reprogramming Disruptiomentioning

confidence: 99%

“…Using this data from two orthogonal screens, we identified strong phenotypic similarities between NCOR1 and OCT4 knockdowns. We have identified functional interactions from knockdowns showing similar phenotypes before [23,24]. Here we characterize the relationship of NCOR1 and OCT4 in early reprogramming.…”

Section: Introductionmentioning

confidence: 97%

See 1 more Smart Citation

NCOR1 and OCT4 Facilitate Early Reprogramming by Co-Suppressing Fibroblast Gene Expression

Peñalosa-Ruiz

Mulder

Veenstra

2019

Preprint

Self Cite

View full text Add to dashboard Cite

Reprogramming somatic cells to induced pluripotent stem cells (iPSC) succeeds only in a small fraction of cells within the population. Reprogramming occurs in distinctive stages, each facing its own bottlenecks. It initiates with overexpression of transcription factors OCT4, SOX2, KLF4 and c-MYC (OSKM) in somatic cells such as mouse embryonic fibroblasts (MEFs). OSKM bind chromatin, silencing the somatic identity and starting the stepwise reactivation of the pluripotency program. However, inefficient suppression of the somatic lineage leads to unwanted epigenetic memory from the tissue of origin, even in successfully generated iPSCs. Thus, it is essential to shed more light on chromatin regulators and processes involved in dissolving the somatic identity. Recent work characterized the role of transcriptional co-repressors NCOR1 and NCOR2 (also known as NCoR and SMRT), showing that they cooperate with c-MYC to silence pluripotency genes during late reprogramming stages. NCOR1/NCOR2 were also proposed to be involved in silencing fibroblast identity, however it is unclear how this happens. Here, we shed light on the role of NCOR1 in early reprogramming. We show that siRNA-mediated ablation of NCOR1 and OCT4 results in very similar phenotypes, including transcriptomic changes and highly correlated high content colony phenotypes. . Both NCOR1 and OCT4 bind to promoters co-occupied by c-MYC in MEFs. During early reprogramming, downregulation of one group of somatic MEF-expressed genes requires both NCOR1 and OCT4, whereas another group of MEF-expressed genes is downregulated by NCOR1 but not OCT4. Our data suggest that NCOR1, assisted by OCT4 and c-MYC, facilitates transcriptional inactivation of genes with high expression in MEFs, which need to be suppressed to bypass an early reprogramming block. This way, NCOR1 facilitates early reprogramming progression.

show abstract

“…These compounds are commonly used to facilitate reprogramming and pluripotent cell culture (Dakhore et al, 2018) and iPSCs generated in this manner are developmentally fully competent (Amlani et al, 2018). 3c reprogramming yields approximately 50 times more stable iPSC colonies than basal reprogramming and does so in a shorter period of time (six rather than twelve days of OKSM expression) (Penalosa-Ruiz et al, 2019;Saunders et al, 2017;Schwarz et al, 2018;Stelzer et al, 2015;Vidal et al, 2014). We therefore speculated that 3c might enhance iPSC formation by counteracting H3K9 methylation more efficiently than OKSM factors alone.…”

Section: Context-dependent Roles Of Ehmt1/2 Activity During Mouse Fibmentioning

confidence: 99%

Context-dependent requirement of H3K9 methyltransferase activity during cellular reprogramming to iPSCs

Vidal

Polyzos

Valencia

et al. 2019

Preprint

View full text Add to dashboard Cite

Methylation of histone 3 at lysine 9 (H3K9) is widely regarded as a major roadblock for cellular reprogramming and interference with associated methyltransferases such as EHMT1 and EHMT2 (also known as GLP and G9A, respectively) increases the efficiencies at which induced pluripotent stem cells (iPSCs) can be derived. Activation of histone and DNA demethylases by ascorbic acid (AA) has become a common approach to facilitate the extensive epigenetic remodeling required for iPSC formation, but possible functional interactions between the H3K9 methylation machinery and AA-stimulated enzymes remain insufficiently explored. Here we show that reduction of EHMT1/2 activity counteracts iPSC formation in an optimized reprogramming system in the presence of AA. Mechanistically, EHMT1/2 activity under these conditions is required for efficient downregulation of somatic genes and transition into an epithelial state. Of note, transient inhibition of EHMT1/2 during reprogramming yields iPSCs that fail to efficiently give rise to viable mice, suggesting persistent molecular defects in these cells.Genetic interference with the H3K9 demethylase KDM3B ameliorated the adverse effect of EHMT1/2 inhibition on iPSC formation. Together, our observations document novel functions of H3K9 methyltransferases during iPSC formation and suggest that the balancing of AAstimulated enzymes by EHMT1/2 supports efficient and error-free iPSC reprogramming to pluripotency.3

show abstract

WDR5, BRCA1, and BARD1 Co-regulate the DNA Damage Response and Modulate the Mesenchymal-to-Epithelial Transition during Early Reprogramming

Cited by 20 publications

References 55 publications

A novel nuclear speckle factor, USP42, promotes homologous recombination repair by resolving DNA double-strand break induced R-loop

A novel nuclear speckle factor, USP42, promotes homologous recombination repair by resolving DNA double-strand break induced R-loop

NCOR1 and OCT4 Facilitate Early Reprogramming by Co-Suppressing Fibroblast Gene Expression

Context-dependent requirement of H3K9 methyltransferase activity during cellular reprogramming to iPSCs

Contact Info

Product

Resources

About