Soluble Nuclear Fraction Research Articles

Abstract P2022: Ankyrin-R Isoforms Are Differentially Expressed In Cardiac Tissues Under Stress

Heart disease remains the leading cause of death in the United States with heart failure specifically accounting for 13.4% of all heart disease related deaths. In 2019, Andersson et al., utilized a multi-omics approach to evaluate participant samples from the Framingham Heart Study and showed that ankyrin-R (AnkR; encoded by ANK1 ) is significantly associated with diastolic function, left ventricular remodeling and heart failure with preserved ejection fraction. Ankyrins are a family of proteins that link integral membrane proteins with the actin/β-spectrin cytoskeleton. Ankyrins-B/G have been extensively studied and identified within the heart and their dysfunction is associated with cardiac structural and electrical phenotypes. Ankyrin-R was first identified in red blood cells and has yet to be studied in the context of cardiac function and heart failure or arrhythmia disease. To study AnkR in the context of the heart we isolated perfused tissues from adult wild-type mice and performed immunoblot and qPCR analysis on ankyrin-R protein and Ank1 mRNA expression. The large AnkR isoform is expressed in the heart, along with the brain, intestine, and spleen. Interestingly, only the heart showed expression of a small AnkR isoform that has previously been shown to interact with the sarcoplasmic protein obscurin. Notably, isolated cardiomyocytes express the small AnkR isoform while cardiac fibroblasts express the canonical large AnkR isoform at both the protein and mRNA level. Canonical AnkR is diffusely expressed in the fibroblast membrane, cytoplasm, cytoskeleton, and soluble nuclear fractions. Interestingly, this expression pattern is switched under stressed conditions where cardiomyocytes increase and cardiac fibroblasts decrease their canonical AnkR expression, respectively. These preliminary results are the first to show canonical AnkR expression in the mouse myocardium specifically within the cardiac fibroblasts and allude that AnkR’s utilization during cardiac stress is cell-type dependent. Future studies will seek to define molecular, cell, and organ phenotypes related to AnkR in the heart.

Effects of ionizing radiation on radio sensitivity of cell nuclei of wheat seedlings

Effects of the 50 Gy and 100 Gy doses of Y-irradiation on radiosensitivity of cell nuclei of soft dwarf wheat seedlings were studied. Changes in the biochemical composition of the nuclear fractions of seedlings of wheat seeds exposed to gamma-irradiation were determined. After exposure to ionizing radiation, total protein and nucleic acids levels appeared to be greater in the soluble nuclear fraction and the nuclear membrane-associated DNA content and proteins increased. It was also found that the value of the dzeta-potential of isolated nuclei of seedlings of irradiated seeds decreased in a static electric field. Changes in the surface charge of the nucleus lead to a violation of its functional activity, since the surface charge of the nuclei is necessary for the normal functioning and regulation of the nuclear-cytoplasmic transport of macromolecules. Exposure to radiation causes destruction of ionogenic groups of molecules of the nuclear membrane, leading to a decrease in the electronegativity of the nuclei, which, in turn, entails a change in the functional activity of the nucleus. The results obtained show that changes in electronegativity and in the content of nuclear fractions are directly dependent on the dose of ionizing radiation. It can be concluded that Y-irradiation in a range from 50 to 100 Gy had beneficial effects on metabolic and proliferative activities of soft wheat cells.

Age-related alterations in protein phosphatase 2A methylation levels in brains of cynomolgus monkeys: a pilot study.

The abnormal activity of PP2A, a dominant member of type 2A serine/threonine protein phosphatase, has been implicated in the development of Alzheimer's disease (AD) and dementia with Lewy bodies (DLB). PP2A is a holoenzyme, and protein methylation of the catalytic subunit, PP2Ac, alters the complex composition. A decrease in PP2Ac methylation levels has been reported in AD and DLB. Aging is the most common risk factor for AD and DLB, but the relationship between aging and PP2A has not been studied in detail. Cynomolgus monkey show increased phosphorylation levels of tau and α-synuclein with aging. In this study, we investigated the alterations in the PP2A activity regulation with aging in monkey brains from 2 to 43years of age using fractionated proteins. We found that type 2A protein phosphatase activity decreased with aging in cytoplasmic and nuclear-soluble fractions. PP2Ac methylation level was decreased in cytoplasmic and sarkosyl-insoluble fractions. A principal component analysis using PP2Ac, demethylated PP2Ac and PP2A methylesterase PME-1 levels in cytoplasmic and nuclear-soluble fractions as attributes showed that aged monkeys were in the same cluster. Our results show that brain aging in cynomolgus monkeys is closely related to changes in PP2A methylation.

Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis.

The nuclear envelope (NE) is central to the architecture of eukaryotic cells, both as a physical barrier separating the nucleus from the cytoplasm and as gatekeeper of selective transport between them. However, in open mitosis, the NE fragments to allow for spindle formation and segregation of chromosomes, resulting in intermixing of nuclear and cytoplasmic soluble fractions. Recent studies have shed new light on the mechanisms driving reinstatement of soluble proteome homeostasis following NE reformation in daughter cells. Here, we provide an overview of how mitotic cells confront this challenge to ensure continuity of basic cellular functions across generations and elaborate on the implications for the proteasome - a macromolecular machine that functions in both cytoplasmic and nuclear compartments.

WHEAT PROTEIN INCREASING THROUGH RADIATION TECHNOLOGIES

The effect of various doses of γ-irradiation on the biochemical composition of the nuclear fractions of wheat seedlings has been investigated. The research results indicate a direct dependence of changes in the biochemical composition of nuclear membranes and soluble nuclear fraction on the magnitude of the radiation dose. A change in the protein content in the fraction of the nuclear membrane and in the soluble nuclear fraction of the cell nuclei of the seedlings of irradiated seeds was observed. The data obtained indicate that ionizing radiation as a result of chain reactions changes the content of nuclear fractions, which in turn leads to a change and disruption of the functional ability of the nucleus.

Glycolytic flux-signaling controls mouse embryo mesoderm development.

How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic PFKFB3 (cytoPFKFB3). Overexpression of cytoPFKFB3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPFKFB3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization.

Nuclear soluble cGAS senses double-stranded DNA virus infection

The DNA sensor cGAS detects cytosolic DNA and instigates type I interferon (IFN) expression. Recent studies find that cGAS also localizes in the nucleus and binds the chromatin. Despite the mechanism controlling nuclear cGAS activation is well elucidated, whether nuclear cGAS participates in DNA sensing is unclear. Here, we report that herpes simplex virus 1 (HSV-1) infection caused the release of cGAS from the chromatin into the nuclear soluble fraction. Like its cytosolic counterpart, the leaked nuclear soluble cGAS also sensed viral DNA, produced cGAMP, and induced mRNA expression of type I IFN and interferon-stimulated genes. Consistently, the nuclear soluble cGAS limited HSV-1 infection. Furthermore, enzyme-deficient mutation (D307A) or cGAS inhibitor RU.251 abolished nuclear cGAS-mediated innate immune responses, suggesting that enzymatic activity is also required for nuclear soluble cGAS. Taken all together, our study demonstrates that nuclear soluble cGAS acts as a nuclear DNA sensor detecting nuclear-replicating DNA viruses.

Nuclear soluble cGAS senses DNA virus infection

Abstract The DNA sensor cGAS detects cytosolic foreign DNA from pathogens or self-DNA from cellular damage and instigates type I interferon (IFN) expression. Recent studies find that cGAS also localizes in the nucleus and tethers to the chromatin. Despite how cGAS is inhibited in the nucleus is well elucidated, whether nuclear cGAS participates in DNA sensing is not clear. Here, we report that herpes simplex virus 1 (HSV-1) infection causes the release of cGAS from the chromatin into the nuclear soluble fraction, and the free nuclear cGAS senses viral DNA to induce innate immune response. We first found that the infection of several HSV-1 strains led to cGAS release from the chromatin in several types of cells, including in RAW264.7 macrophages, THP-1 monocytes, and bone marrow-derived macrophages. DNA damage agent cisplatin failed to induce nuclear soluble cGAS, suggesting that cGAS release from the chromatin is not due to DNA damage or apoptosis. Interestingly, inhibition of HSV-1 replication blocked the release of nuclear soluble cGAS. To determine the role of nuclear cGAS in DNA virus infection, we reconstituted a Dox-induced nuclear-only cGAS mutant into cGAS knockout RAW264.7 cells. After induction, only chromatin-bound cGAS was found in the reconstituted cells. Similarly, HSV-1 infected also induced nuclear soluble cGAS in this cell line. More importantly, the nuclear-only cGAS stable cells limited HSV-1 infection by producing cGAMP and inducing mRNA expression of type I IFN and interferon-stimulated genes. Taken all together, our study demonstrates that nuclear soluble cGAS is a DNA sensor inside the nucleus. This research was funded by the National Institutes of Health (R21AI137750 and R01AI141399 to S.L.).

Methods to separate nuclear soluble fractions reflecting localizations in living cells

To understand various intranuclear functions, it is important to know when, what, and how proteins enter the nucleus. Although many methods and commercial kits for nuclear fractionation have been developed, there are still no methods for obtaining a complete nuclear proteome. Soluble nuclear proteins are often lost during fractionation. We developed remarkably improved methods to obtain nuclear soluble fractions by optimizing the conditions of selective permeabilization of the plasma membrane. As a result, 10 million cells could be separated into the cytoplasmic and nuclear soluble fractions more precisely in a 1.5-mL test tube. Moreover, the addition of an inhibitor to prevent leakage from the nucleus retained small proteins in the nucleus. Because of the simple protocols and easy application for multiple samples, our methods are expected to be applied to various studies on spatiotemporal changes of dynamic nuclear proteins, such as signal transduction.

Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation

Rif1 regulates DNA replication timing and double-strand break repair, and its depletion induces transcriptional bursting of two-cell (2C) zygote-specific genes in mouse ES cells. However, how Rif1 regulates zygotic transcription is unclear. We show here that Rif1 depletion promotes the formation of a unique Zscan4 enhancer structure harboring both histone H3 lysine 27 acetylation (H3K27ac) and moderate levels of silencing chromatin mark H3K9me3. Curiously, another enhancer mark H3K4me1 is missing, whereas DNA methylation is still maintained in the structure, which spreads across gene bodies and neighboring regions within the Zscan4 gene cluster. We also found by function analyses of Rif1 domains in ES cells that ectopic expression of Rif1 lacking N-terminal domain results in upregulation of 2C transcripts. This appears to be caused by dominant negative inhibition of endogenous Rif1 protein localization at the nuclear periphery through formation of hetero-oligomers between the N-terminally truncated and endogenous forms. Strikingly, in murine 2C embryos, most of Rif1-derived polypeptides are expressed as truncated forms in soluble nuclear or cytosolic fraction and are likely nonfunctional. Toward the morula stage, the full-length form of Rif1 gradually increased. Our results suggest that the absence of the functional full-length Rif1 due to its instability or alternative splicing and potential inactivation of Rif1 through dominant inhibition by N-terminally truncated Rif1 polypeptides may be involved in 2C-specific transcription program.

MP66-04 THE ROLE OF CHROMATIN AND HISTONE SUCCINYLATION AS A POST-TRANSLATIONAL MODIFICATION IN NON-MUSCLE INVASIVE BLADDER CANCER

You have accessJournal of UrologyBladder Cancer: Basic Research & Pathophysiology III (MP66)1 Sep 2021MP66-04 THE ROLE OF CHROMATIN AND HISTONE SUCCINYLATION AS A POST-TRANSLATIONAL MODIFICATION IN NON-MUSCLE INVASIVE BLADDER CANCER Genesis Rivera-Marquez, Beatriz Walter, Maria Merino, and Vladimir Valera Genesis Rivera-MarquezGenesis Rivera-Marquez More articles by this author , Beatriz WalterBeatriz Walter More articles by this author , Maria MerinoMaria Merino More articles by this author , and Vladimir ValeraVladimir Valera More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002106.04AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Bladder cancer has been characterized as one of the most genomically unstable cancers. Epigenetic events such as DNA methylation and histone acetylation have been described to play key roles in the disease onset and progression. These events are controlled ultimately by post-translational modifications (PTM) of proteins. In this study, we aimed to characterize a recently described PTM such as protein succinylation and its role in non-muscle invasive bladder cancer pathogenesis. METHODS: Well-characterized cell lines representing non-muscle invasive bladder cancer including MGH-U3 (pTa/pT1-derived), T24 (pTa-derived), RT4 (pT1-derived), RT-112 (pTa) were analyzed. Additionally, two muscle-invasive cancer derived cell lines UM-UC3 and SW-780 were included for comparison. All analysis were normalized to the reference Primary Bladder Epithelial cells (untransformed). Cell compartment fractionation was achieved by centrifugation under detergent, and included cell membrane, cytoplasmic, nuclear soluble and chromatin fractions. Extracts were then probed with Anti-Pan-Succinyl Lysine antibody. Histone-3 Acetylation and methylation were also tested. Chromatin immunoprecipitation with pan-succinyl-lysine was then performed and genomic DNA sent for Next Generation Sequencing (Chip-Seq) to identify transcription factors bound to succinylated chromatin. RESULTS: All cell compartments contained succinylated proteins, predominantly the cytosolic and chromatin/histone fractions. Histone-3 succinylation was prominent in all cancer cell lines predominantly the NMIBC ones. However, there was no clear association between succinylation and p53 and/or FGFR3 mutation status. Chip-seq analysis demonstrated that most of the represented marks on sequencing mapped to intergenic regions (>50%) and were associated with euchromatin markers, i.e, associated with gene activation. Metabolomic profiling of the cells also varied, ranging from mostly glycolytic pattern to predominatly ox-phos dependent. Accumulation of TCA-intermediaries such as Acetyl-Co-A, Fumarate, Citrate, and Succinate was marked in the NMIBC cells. CONCLUSIONS: Our results suggests that succinylation of chromatin components may be important for regulating nuclear functions, including chromatin dynamics and transcription and therefore in the pathogenesis of non-muscle invasive bladder cancer. Source of Funding: NIH Intramural Research Program © 2021 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 206Issue Supplement 3September 2021Page: e1130-e1130 Advertisement Copyright & Permissions© 2021 by American Urological Association Education and Research, Inc.MetricsAuthor Information Genesis Rivera-Marquez More articles by this author Beatriz Walter More articles by this author Maria Merino More articles by this author Vladimir Valera More articles by this author Expand All Advertisement Loading ...

FoxA2 and RNA Pol II mediate human islet amyloid polypeptide turnover in ER-stressed pancreatic β-cells.

Here, we investigated transcriptional and trafficking mechanisms of human islet amyloid polypeptide (hIAPP) in normal and stressed β-cells. In high glucose-challenged human islets and rat insulinoma cells overexpressing hIAPP, cell fractionation studies revealed increased accumulation of hIAPP. Unexpectedly, a significant fraction (up to 22%) of hIAPP was found in the nuclear soluble and chromatin-enriched fractions of cultured human islet and rat insulinoma cells. The nucleolar accumulation of monomeric forms of hIAPP did not have any adverse effect on the proliferation of β-cells nor did it affect nucleolar organization or function. However, intact nucleolar organization and function were essential for hIAPP expression under normal and ER-stress conditions as RNA polymerase II inhibitor, α-amanitin, reduced hIAPP protein expression evoked by high glucose and thapsigargin. Promoter activity studies revealed the essential role of transcription factor FoxA2 in hIAPP promoter activation in ER-stressed β-cells. Transcriptome and secretory studies demonstrate that the biosynthetic and secretory capacity of islet β-cells was preserved during ER stress. Thus, the main reason for increased intracellular hIAPP accumulation is its enhanced biosynthesis under these adverse conditions.

USP13 interacts with cohesin and regulates its ubiquitination in human cells

Cohesin is a multiprotein ring complex that regulates 3D genome organization, sister chromatid cohesion, gene expression, and DNA repair. Cohesin is known to be ubiquitinated, although the mechanism, regulation, and effects of cohesin ubiquitination remain poorly defined. We previously used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in human HCT116 cells. Here we report that mass spectrometry analysis of dual-affinity purifications identified the USP13 deubiquitinase as a novel cohesin-interacting protein. Subsequent immunoprecipitation/Western blots confirmed the endogenous interaction in HCT116, 293T, HeLa, and RPE-hTERT cells; demonstrated that the interaction occurs specifically in the soluble nuclear fraction (not in the chromatin); requires the ubiquitin-binding domains (UBA1/2) of USP13; and occurs preferentially during DNA replication. Reciprocal dual-affinity purification of endogenous USP13 followed by mass spectrometry demonstrated that cohesin is its primary interactor in the nucleus. Ectopic expression and CRISPR knockout of USP13 showed that USP13 is paradoxically required for both deubiquitination and ubiquitination of cohesin subunits in human cells. USP13 was dispensable for sister chromatid cohesion in HCT116 and HeLa cells, whereas it was required for the dissociation of cohesin from chromatin as cells transit through mitosis. Together these results identify USP13 as a new cohesin-interacting protein that regulates the ubiquitination of cohesin and its cell cycle regulated interaction with chromatin.

Nuclear Soluble cGAS Senses DNA Virus Infection

The cytosolic DNA sensor cGAS detects foreign DNA from pathogens or self-DNA from cellular damage and instigates type I interferon (IFN) expression. Recent studies find that cGAS also localizes in the nucleus and binds the chromatin. Despite how cGAS is inhibited in the nucleus is well elucidated, whether nuclear cGAS participates in DNA sensing is not clear. Here, we report that herpes simplex virus 1 (HSV-1) infection caused the release of cGAS from the chromatin into the nuclear soluble fraction. Like its cytosolic counterpart, the leaked nuclear soluble cGAS could sense viral DNA, produce cGAMP, and induce mRNA expression of type I IFN and interferon-stimulated genes. Furthermore, the nuclear cGAS limited HSV-1 infection. Taken together, our study demonstrates that HSV-1 infection releases cGAS from the chromatin tethering and, in turn, the nuclear soluble cGAS activates type I IFN production.

NCAPH Recruits and Stabilizes GEN1 in Chromatin to Facilitate DNA Interstrand Crosslink Repair

Repairing damaged DNA and removing all physical connections between sister chromosomes is important for proper chromosomal segregation by contributing to chromosomal stability. Here, we show that depletion of NCAPH exacerbates chromosome segregation errors and cytokinesis failure due to sister-chromatid intertwinement, which is distinct form the ultrafine DNA bridges (UFB) induced by DNA inter-strand crosslinks (DNA-ICL). Importantly, we identified an interaction between NCAPH and GEN1 in the chromatin via binding at the N-terminus of NCAPH. DNA-ICL activation, using ICL-inducing agents, increased the expression and interaction between NCAPH and GEN1 in the soluble nuclear and chromatin fractions, indicating that the NCAPH-GEN1 interaction participates in repairing DNA-ICLs. Moreover, NCAPH recruits and stabilizes GEN1 within chromatin at the G2/M phase, and is associated with DNA-ICL induced damage repair. Therefore, NCAPH-GEN1 specifically responds to DNA-ICLs, and NCAPH recruits and stabilizes GEN1 to ensure DNA damage repair and proper chromosome separation.

Macrophage migration inhibitory factor is differentially expressed in normal and choriocarcinoma trophoblast cells.

Trophoblast cells are specific for placenta, the organ necessary for development of the fetus. Trophoblast derived choriocarcinoma is a rare cancer, with high metastatic potential, invading surrounding tissues and distant organs. Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine involved in a wide range of biological processes, which is increased in almost all human cancers. Expression of MIF in normal and choriocarcinoma trophoblast cells is investigated here, using normal extravillous trophoblast derived cell line HTR-8/SVneo, and choriocarcinoma cell lines JAR and JEG3. Expression of MIF and its receptors CD74 and CXCR2 was investigated at mRNA level using qPCR. Expression of MIF protein was studied using immunofluorescence and western blot, under reducing and native conditions, in whole cell lysates, subcellular fractions and conditioned media. The expression of MIF mRNA was similar in all three cell lines, while CD74 mRNA was more expressed in choriocarcinoma cells (14-fold for JAR, 12-fold for JEG3, p<0.01). CXCR2 mRNA was higher in JEG3 cell line compared to HTR-8/SVneo cells (6-fold, p<0.01). While the cellular level of MIF was similar, the level of secreted MIF was lower in JAR cell conditioned media compared to media of both HTR-8/SVneo (2.8-fold, p<0.01) and JEG3 cells (4.1-fold, p<0.001). Cellular distribution of MIF was similar between the studied cell types. MIF was predominantly cytoplasmic, but also detected in membrane, nuclear soluble and nuclear chromatin fraction. MIF appeared in high molecular weight complexes of >150 kDa under native conditions. A band of 140-145 kDa was consistently present in JEG3 cell lysates, while it was absent or very weak in other cell types. These results show that MIF/CD74 axis is shifted in choriocarcinoma, as previously shown for other cancers, and further justifies research towards the most effective MIF targeting therapeutics.

Biosynthesis of O-N-acetylgalactosamine glycans in the human cell nucleus

Biological functions of nuclear proteins are regulated by post-translational modifications (PTMs) that modulate gene expression and cellular physiology. However, the role of O-linked glycosylation (O-GalNAc) as a PTM of nuclear proteins in the human cell has not been previously reported. Here, we examined in detail the initiation of O-GalNAc glycan biosynthesis, representing a novel PTM of nuclear proteins in the nucleus of human cells, with an emphasis on HeLa cells. Using soluble nuclear fractions from purified nuclei, enzymatic assays, fluorescence microscopy, affinity chromatography, MS, and FRET analyses, we identified all factors required for biosynthesis of O-GalNAc glycans in nuclei: the donor substrate (UDP-GalNAc), nuclear polypeptide GalNAc -transferase activity, and a GalNAc transferase (polypeptide GalNAc-T3). Moreover, we identified O-GalNAc glycosylated proteins in the nucleus and present solid evidence for O-GalNAc glycan synthesis in this organelle. The demonstration of O-GalNAc glycosylation of nuclear proteins in mammalian cells reported here has important implications for cell and chemical biology.

Characterization of Posttranslational Modifications on Histone Variants.

The study of histone variants and histone posttranslational modifications (PTMs) is a trending topic in different fields including developmental biology, neurobiology, and immunology; as well as in the understanding of molecular mechanisms leading to diverse diseases, such as cancer. Since the establishment of histone PTMs starts immediately after their synthesis and it continues once they are assembled into chromatin, here we describe a classic protocol of subcellular fractionation aiming to study histones at different stages of maturation. This includes newly synthesized histones enriched in cytosolic fractions; a pool of newly synthesized, evicted, and stored histones enriched in nuclear soluble fractions; and chromatin-associated histones enriched in chromatin pellet. To study specific histone variants and the establishment of their PTMs, we describe a protocol for obtaining histone variants expressed in bacteria. In addition, we describe a Triton-Acetic acid-Urea (TAU) gel electrophoresis protocol adapted to work on mini-gels, which can be coupled to Western blot to analyze PTMs on histone variants. Finally, we describe a Chromatin immunoprecipitation (ChIP) assay for studying histone PTMs, or tagged histone variants, on specific DNA sequences.

TIRR regulates 53BP1 by masking its histone methyl-lysine binding function.

P53-binding protein 1 (53BP1) is a multi-functional double-strand break repair protein that is essential for class switch recombination in B lymphocytes and for sensitizing BRCA1-deficient tumours to poly-ADP-ribose polymerase-1 (PARP) inhibitors. Central to all 53BP1 activities is its recruitment to double-strand breaks via the interaction of the tandem Tudor domain with dimethylated lysine 20 of histone H4 (H4K20me2). Here we identify an uncharacterized protein, Tudor interacting repair regulator (TIRR), that directly binds the tandem Tudor domain and masks its H4K20me2 binding motif. Upon DNA damage, the protein kinase ataxia-telangiectasia mutated (ATM) phosphorylates 53BP1 and recruits RAP1-interacting factor 1 (RIF1) to dissociate the 53BP1-TIRR complex. However, overexpression of TIRR impedes 53BP1 function by blocking its localization to double-strand breaks. Depletion of TIRR destabilizes 53BP1 in the nuclear-soluble fraction and alters the double-strand break-induced protein complex centring 53BP1. These findings identify TIRR as a new factor that influences double-strand break repair using a unique mechanism of masking the histone methyl-lysine binding function of 53BP1.

Successes and Challenges of PARP Inhibitors in Cancer Therapy.

Successes and Challenges of PARP Inhibitors in Cancer Therapy.