Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA197260 | ENA |
REPOSITORIES: ENA
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Project description:WIP1 phosphatase is emerging as an important regulator of tumorigenesis, but no unifying mechanistic network has been proposed. Here we found that WIP1 plays a key role in the transcriptional regulation of heterochromatin-associated DNA sequences in germ-line and cancer cells. WIP1 was required for epigenetic remodeling of repetitive DNA elements within the heterochromatin, including L1 LINE retrotransposons. Mechanistically, WIP1regulated an ATM-dependent increase in BRCA1 occupancy on L1 LINEs, resulting in closed chromatin without ubiquitination of histone H2A. This mechanism appeared to be dependent on the ability of BRCA1 to bind the heterochromatin protein HP1, the recruitment of DNA methyltransferases, and subsequent DNA methylation. Attenuation of ATM, in turn, reversed heterochromatin methylation in both germ-line and cancer cells. DNA methylation plays a central role in the generation of mutations in human tumors and we found that WIP1 levels strongly correlated with C-to-T substitutions and a total mutation load in primary breast cancers. We propose that WIP1 plays an important role in the regulation of DNA methylation and global heterochromatin silencing, and thus is critical in maintaining genome integrity during development and in cancer. Total RNA was extracted from control spermatids, Wip1-/- and Wip1-/- Atm+/- spermatids. The final cRNA samples were hybridized in triplicates to Illumina Mouse WG-6 v2.0 Expression arrays.
2013-10-19 | E-GEOD-46103 | biostudies-arrayexpress
Project description:WIP1 phosphatase is emerging as an important regulator of tumorigenesis, but no unifying mechanistic network has been proposed. Here we found that WIP1 plays a key role in the transcriptional regulation of heterochromatin-associated DNA sequences in germ-line and cancer cells. WIP1 was required for epigenetic remodeling of repetitive DNA elements within the heterochromatin, including L1 LINE retrotransposons. Mechanistically, WIP1regulated an ATM-dependent increase in BRCA1 occupancy on L1 LINEs, resulting in closed chromatin without ubiquitination of histone H2A. This mechanism appeared to be dependent on the ability of BRCA1 to bind the heterochromatin protein HP1, the recruitment of DNA methyltransferases, and subsequent DNA methylation. Attenuation of ATM, in turn, reversed heterochromatin methylation in both germ-line and cancer cells. DNA methylation plays a central role in the generation of mutations in human tumors and we found that WIP1 levels strongly correlated with C-to-T substitutions and a total mutation load in primary breast cancers. We propose that WIP1 plays an important role in the regulation of DNA methylation and global heterochromatin silencing, and thus is critical in maintaining genome integrity during development and in cancer.
2013-10-19 | GSE46103 | GEO
Project description:Jaiswal2017 - Cell cycle arrest
This model is described in the article:
ATM/Wip1 activities at
chromatin control Plk1 re-activation to determine G2 checkpoint
duration.
Jaiswal H, Benada J, Müllers E,
Akopyan K, Burdova K, Koolmeister T, Helleday T, Medema RH,
Macurek L, Lindqvist A.
EMBO J. 2017 Jul; 36(14):
2161-2176
Abstract:
After DNA damage, the cell cycle is arrested to avoid
propagation of mutations. Arrest in G2 phase is initiated by
ATM-/ATR-dependent signaling that inhibits mitosis-promoting
kinases such as Plk1. At the same time, Plk1 can counteract
ATR-dependent signaling and is required for eventual resumption
of the cell cycle. However, what determines when Plk1 activity
can resume remains unclear. Here, we use FRET-based reporters
to show that a global spread of ATM activity on chromatin and
phosphorylation of ATM targets including KAP1 control Plk1
re-activation. These phosphorylations are rapidly counteracted
by the chromatin-bound phosphatase Wip1, allowing cell cycle
restart despite persistent ATM activity present at DNA lesions.
Combining experimental data and mathematical modeling, we
propose a model for how the minimal duration of cell cycle
arrest is controlled. Our model shows how cell cycle restart
can occur before completion of DNA repair and suggests a
mechanism for checkpoint adaptation in human cells.
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BIOMD0000000641.
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2014-03-28 | BIOMD0000000641 | BioModels
Project description:The number of newly-formed neurons declines rapidly during aging. Here we describe an important mechanism that contributes to this decline via Wip1-dependent regulation of neuronal differentiation. We found that Wip1 is expressed in neural stem/progenitor cells (NPCs) of the mouse subventricular zone and its upregulation at physiological levels maintained higher NPC numbers and neuronal differentiation in old mice. This resulted in markedly improved neuron formation and rescued a functional defect in fine odor discrimination in old mice. We identified Dkk3 as a key downstream target of Wip1 and found that its expression in SVZ is restricted to NPCs. Functionally, Dkk3 inhibited neuroblast formation by suppressing Wnt signaling, while deletion of Dkk3 or pharmacological reactivation of the Wnt pathway improved neuron formation and olfactory function in aged mice. We propose that Wip1 controls a Dkk3-dependent inhibition of neuronal differentiation during aging and thus regulating Wip1 levels could prevent certain aspects of functional decline of the aging brain. We found if neurospheres were derived from 18 months old mice, Wip1 transgenic neurospheres were more neurogenic than wt ones. This microarray was a pilot experiment to search the mechanism how Wip1 Transgene promoted neurogenesis, and found Dkk3 as a potential mediator. WT vs Wip1Tg neurospheres were cultured from mouse brain, and gene expression was compared using Illumina mouseWG-6 array
2014-04-26 | E-GEOD-57105 | biostudies-arrayexpress
Project description:Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites. In total 44 samples; 2 replicates for each genotype and for each ChIP (HP1a, H3K9me2 and H3K9me3)
2012-12-21 | E-GEOD-38366 | biostudies-arrayexpress
Project description:The number of newly-formed neurons declines rapidly during aging. Here we describe an important mechanism that contributes to this decline via Wip1-dependent regulation of neuronal differentiation. We found that Wip1 is expressed in neural stem/progenitor cells (NPCs) of the mouse subventricular zone and its upregulation at physiological levels maintained higher NPC numbers and neuronal differentiation in old mice. This resulted in markedly improved neuron formation and rescued a functional defect in fine odor discrimination in old mice. We identified Dkk3 as a key downstream target of Wip1 and found that its expression in SVZ is restricted to NPCs. Functionally, Dkk3 inhibited neuroblast formation by suppressing Wnt signaling, while deletion of Dkk3 or pharmacological reactivation of the Wnt pathway improved neuron formation and olfactory function in aged mice. We propose that Wip1 controls a Dkk3-dependent inhibition of neuronal differentiation during aging and thus regulating Wip1 levels could prevent certain aspects of functional decline of the aging brain. We found if neurospheres were derived from 18 months old mice, Wip1 transgenic neurospheres were more neurogenic than wt ones. This microarray was a pilot experiment to search the mechanism how Wip1 Transgene promoted neurogenesis, and found Dkk3 as a potential mediator.
2014-04-26 | GSE57105 | GEO
Project description:Epe1 histone demethylase restricts H3K9-methylation-dependent heterochromatin, preventing it from spreading over, and silencing, gene-containing regions in fission yeast. External stress induces an adaptive response allowing heterochromatin island formation that confers resistance on surviving wild-type lineages. Here we investigate the mechanism by which Epe1 is regulated in response to stress. Exposure to caffeine or antifungals results in Epe1 ubiquitylation and proteasome-dependent removal of the N-terminal 150 residues from Epe1, generating truncated tEpe1 which accumulates in the cytoplasm. Constitutive tEpe1 expression increases H3K9 methylation over several chromosomal regions, reducing expression of underlying genes and enhancing resistance. Reciprocally, constitutive non-cleavable Epe1 expression decreases resistance. tEpe1-mediated resistance requires a functional JmjC demethylase domain. Moreover, caffeine-induced Epe1-to-tEpe1 cleavage is dependent on an intact cell-integrity MAP kinase stress signalling pathway, mutations in which alter resistance. Thus, environmental changes provoke a mechanism that curtails the function of this key epigenetic modifier, allowing heterochromatin to reprogram gene expression, thereby bestowing resistance to some cells within a population. H3K9me-heterochromatin components are conserved in human and crop plant fungal pathogens for which a limited number of antifungals exist. Our findings reveal how transient heterochromatin-dependent antifungal resistant epimutations develop and thus inform on how they might be countered.
2022-10-13 | PXD030205 | Pride
Project description:Bilaterality of breast cancer is an indicator of constitutional cancer susceptibility, however, the molecular causes underlying this predisposition in the majority of cases is not known. We hypothesize that epigenetic misregulation of cancer related genes could partially account for this predisposition. We have performed methylation microarray analysis of peripheral blood DNA from 14 women with bilateral breast cancer compared to 14 unaffected matched controls throughout 17 candidate breast cancer susceptibility genes including BRCA1, BRCA2, CHEK2, ATM, ESR1, SFN, CDKN2A, TP53, GSTP1, CDH1, CDH13, HIC1, PGR, SFRP1, MLH1, RARB and HSD17B4. We show that the majority of methylation variability is associated with intragenic repetitive elements. Detailed validation of the tiled region around ATM was performed by bisulfite modification and pyrosequencing of the same samples and in a second set of peripheral blood DNA from 190 bilateral breast cancer patients compared to 190 controls. We show significant hypermethylation of one intragenic repetitive element in breast cancer cases compared to controls (p=0.0017) with the highest quartile of methylation associated with a three-fold increased risk of breast cancer (OR = 3.20, 95% C.I.=1.78-5.86, p=0.000083). Increased methylation of this locus is associated with lower steady state ATM mRNA level and correlates with age of cancer patients but not controls, suggesting a combined age-phenotype related association. This research demonstrates the potential for gene-body epigenetic misregulation of ATM and other cancer related genes in peripheral blood DNA that may be useful as a novel marker to estimate breast cancer risk. Keywords: Differential Methylation Hybridisation
2009-01-29 | GSE14603 | GEO
Project description:Constitutive domains of repressive heterochromatin are maintained within the fission yeast genome through self-reinforcing mechanisms involving histone methylation and small RNAs. Non-coding RNAs generated from heterochromatic regions are processed into small RNAs by the RNA interference pathway, and are subject to silencing through both transcriptional and post-transcriptional mechanisms. While the pathways involved in maintenance of the repressive heterochromatin state are reasonably well understood, less is known about the requirements for its establishment. Here we describe a novel role for the post-transcriptional regulatory factor Mkt1 in establishment of heterochromatin at pericentromeres in fission yeast. Loss of Mkt1 does not affect maintenance of existing heterochromatin, but does affect its recovery following depletion, as well as de novo establishment of heterochromatin on a mini-chromosome. Pathway dissection revealed that Mkt1 is required for RNAi-mediated post-transcriptional silencing, downstream of small RNA production. Mkt1 physically associates with pericentromeric transcripts, and is additionally required for maintenance of silencing and heterochromatin at centromeres when transcriptional silencing is impaired. Our findings provide new insight into the mechanism of RNAi-mediated post-transcriptional silencing in fission yeast, and unveil an important role for post-transcriptional silencing in establishment of heterochromatin that is dispensable when full transcriptional silencing is imposed.
2019-11-28 | PXD015484 | Pride
Project description:Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites.
2012-12-21 | GSE38366 | GEO