• HGF/SF
• fibroblasts
• squamous cell carcinoma
• xeroderma pigmentosum

• ANR-11-LABX-0028-01 French Government (National Research Agency, ANR; CNRS; INSERM) through the 'Invest-ments for the Future' LABEX SIGNALIFE
• ARC, SFI201212055859 Association pour la Recherche contre le Cancer
• n°174761, UMR7284 Société Française de Dermatologie

• Rad4
• X-ray crystallography
• XPC
• gene mutation
• homology model
• nucleotide excision repair
• polymorphism
• xeroderma pigmentosum

• Animals
• Humans
• Xeroderma Pigmentosum/metabolism
• Excision Repair
• DNA-Binding Proteins/chemistry
• DNA Repair/genetics
• Mutation
• Neoplasms
• Nucleotides
• Mammals/metabolism

• R15 GM147899 NIGMS NIH HHS

• Hes5
• SOX15
• SOX2
• coactivator
• iPSC
• neural differentiation
• pluripotency
• reprogramming
• trascription

The XPC protein complex plays a central role in DNA lesion recognition for global genome nucleotide excision repair (GG-NER). Lesion recognition can be accomplished in either a UV-DDB-dependent or -independent manner; however, it is unclear how these sub-pathways are regulated in chromatin. Here, we show that histone deacetylases 1 and 2 facilitate UV-DDB-independent recruitment of XPC to DNA damage by inducing histone deacetylation. XPC localizes to hypoacetylated chromatin domains in a DNA damage-independent manner, mediated by its structurally disordered middle (M) region. The M region interacts directly with the N-terminal tail of histone H3, an interaction compromised by H3 acetylation. Although the M region is dispensable for in vitro NER, it promotes DNA damage removal by GG-NER in vivo, particularly in the absence of UV-DDB. We propose that histone deacetylation around DNA damage facilitates the recruitment of XPC through the M region, contributing to efficient lesion recognition and initiation of GG-NER.

•

Histone deacetylation by HDAC1/2 promotes the DNA lesion recognition by XPC

• DNA repair protein
• Embryonic stem cell
• Neural progenitor cell
• PARP1
• Pluripotent stem cell
• SOX2
• Transcriptional regulation

• x-ray crystallography
• virus-host interactions
• viral proteins
• solution-state nmr

SRY-box 2 (Sox2) is a transcription factor with critical roles in maintaining embryonic stem (ES) cell and adult stem cell functions and in tumorigenesis. However, how Sox2 exerts its transcriptional function remains unclear. Here, we used an in vitro protein–protein interaction assay to discover transcriptional regulators for ES cell core transcription factors (Oct4, Sox2, Klf4, and c-Myc) and identified members of the steroid receptor coactivators (SRCs) as Sox2-specific interacting proteins. The SRC family coactivators have broad roles in transcriptional regulation, but it is unknown whether they also serve as Sox2 coactivators. We demonstrated that these proteins facilitate Sox2 transcriptional activity and act synergistically with p300. Furthermore, we uncovered an acetylation-enhanced interaction between Sox2 and SRC-2/3, but not SRC-1, demonstrating it is Sox2 acetylation that promotes the interaction. We identified putative Sox2 acetylation sites required for acetylation-enhanced interaction between Sox2 and SRC-3 and demonstrated that acetylation on these sites contributes to Sox2 transcriptional activity and recruitment of SRC-3. We showed that activation domains 1 and 2 of SRC-3 both display a preferential binding to acetylated Sox2. Finally, functional analyses in mouse ES cells demonstrated that knockdown of SRC-2/3 but not SRC-1 in mouse ES cells significantly downregulates the transcriptional activities of various Sox2 target genes and impairs ES cell stemness. Taken together, we identify specific SRC family proteins as novel Sox2 coactivators and uncover the role of Sox2 acetylation in promoting coactivator recruitment and Sox2 transcriptional function.

• SRC-1
• SRC-2
• SRC-3
• Sox2 acetylation
• Steroid receptor coactivators
• p300
• pluripotency
• transcription

• Acetylation
• Animals
• HEK293 Cells
• HeLa Cells
• Humans
• Mice
• Nuclear Receptor Coactivator 1/genetics
• Nuclear Receptor Coactivator 1/metabolism
• Nuclear Receptor Coactivator 2/genetics
• Nuclear Receptor Coactivator 2/metabolism
• Nuclear Receptor Coactivator 3/genetics
• Nuclear Receptor Coactivator 3/metabolism
• SOXB1 Transcription Factors/genetics
• SOXB1 Transcription Factors/metabolism
• Transcription, Genetic

• DNA damage recognition
• Fluorescence lifetime
• Förster resonance energy transfer
• Molecular dynamics simulation
• Nucleotide excision repair
• Protein-DNA interaction
• Rad4
• Sequence impact
• Time-resolved fluorescence
• XPC
• Xeroderma pigmentosum
• x-ray crystallography

• Base Sequence
• DNA/metabolism
• DNA/chemistry
• DNA Damage
• DNA Repair
• DNA-Binding Proteins/metabolism
• DNA-Binding Proteins/chemistry
• Molecular Dynamics Simulation
• Nucleic Acid Conformation
• Protein Binding
• Saccharomyces cerevisiae/metabolism
• Saccharomyces cerevisiae/genetics
• Saccharomyces cerevisiae Proteins/metabolism
• Saccharomyces cerevisiae Proteins/chemistry

• R01 ES025987 NIEHS NIH HHS
• R01 HG006827 NHGRI NIH HHS
• R21 ES028384 NIEHS NIH HHS
• Howard Hughes Medical Institute

• R01 HL125527 NHLBI NIH HHS
• NIH Office of the Director
• Charles H. Hood Foundation
• Brigham and Women’s Hospital
• Harvard Stem Cell Institute
• Brigham Research Institute
• Boston Biomedical Innovation Center

• DNA damage response
• Embryonic stem cell
• Liquid-liquid phase separation
• Low complexity domain
• Pluripotency
• Transcription

• R01 HL125527 NHLBI NIH HHS

In addition to nucleosomes, chromatin contains non-histone chromatin-associated proteins, of which the high-mobility group proteins are the most abundant. Chromatin-mediated regulation of transcription involves DNA methylation and histone modifications. However, the order of events and the precise function of high-mobility group proteins during transcription initiation remain unclear. Here we show that high-mobility group AT-hook 2 protein (HMGA2) induces DNA nicks at the transcription start site, which are required by the histone chaperone FACT complex to incorporate nucleosomes containing the histone variant H2A.X. Further, phosphorylation of H2A.X at S139 (γ-H2AX) is required for repair-mediated DNA demethylation and transcription activation. The relevance of these findings is demonstrated within the context of TGFB1 signaling and idiopathic pulmonary fibrosis, suggesting therapies against this lethal disease. Our data support the concept that chromatin opening during transcriptional initiation involves intermediates with DNA breaks that subsequently require DNA repair mechanisms to ensure genome integrity.

The order of DNA methylation and histone modifications during transcription remained unclear. Here the authors show that HMGA2 induces DNA nicks at TGFB1-responsive genes, promoting nucleosome incorporation containing γ-H2AX, which is required for repair-mediated DNA demethylation and transcription.

• Base Sequence
• Binding Sites
• Crystallography, X-Ray
• DNA/chemistry
• DNA/genetics
• DNA/metabolism
• DNA Damage
• DNA Repair
• DNA, Fungal/chemistry
• DNA, Fungal/genetics
• DNA, Fungal/metabolism
• DNA-Binding Proteins/chemistry
• DNA-Binding Proteins/genetics
• DNA-Binding Proteins/metabolism
• Kinetics
• Molecular Dynamics Simulation
• Mutation
• Nucleic Acid Conformation
• Organophosphorus Compounds/chemical synthesis
• Organophosphorus Compounds/metabolism
• Protein Binding
• Protein Conformation, alpha-Helical
• Protein Conformation, beta-Strand
• Protein Interaction Domains and Motifs
• Saccharomyces cerevisiae/genetics
• Saccharomyces cerevisiae/metabolism
• Saccharomyces cerevisiae Proteins/chemistry
• Saccharomyces cerevisiae Proteins/genetics
• Saccharomyces cerevisiae Proteins/metabolism
• Spectrometry, Fluorescence
• Substrate Specificity
• Thermodynamics

• R01 ES025987 NIEHS NIH HHS
• R01 HG006827 NHGRI NIH HHS
• Howard Hughes Medical Institute
• R21 ES028384 NIEHS NIH HHS
• National Science Foundation
• National Institutes of Health
• New York University

• dedifferentiation
• dopamine receptor antagonist
• glioblastoma
• glioma-initiating cells
• radiation

• Animals
• Brain Neoplasms/drug therapy
• Brain Neoplasms/metabolism
• Brain Neoplasms/pathology
• Brain Neoplasms/radiotherapy
• Disease Models, Animal
• Dopamine Antagonists/pharmacology
• Dopamine Antagonists/therapeutic use
• Gene Expression Regulation, Neoplastic
• Glioblastoma/drug therapy
• Glioblastoma/metabolism
• Glioblastoma/pathology
• Glioblastoma/radiotherapy
• Glioma/drug therapy
• Glioma/metabolism
• Glioma/pathology
• Glioma/radiotherapy
• Glycogen Synthase Kinase 3/metabolism
• Mice
• Mice, Inbred C57BL
• Mice, Inbred NOD
• Mice, SCID
• Phenotype
• RNA, Messenger/metabolism
• Radiation Tolerance
• Receptors, Dopamine/drug effects
• SOXB1 Transcription Factors
• Trifluoperazine/pharmacology
• Trifluoperazine/therapeutic use
• Xenograft Model Antitumor Assays
• beta Catenin

• R01 CA200234 NCI NIH HHS
• P30 CA016042 NCI NIH HHS
• R01 CA137110 NCI NIH HHS
• R01 CA161294 NCI NIH HHS
• P50 CA211015 NCI NIH HHS

The nucleotide excision repair (NER) pathway is activated in response to a broad spectrum of DNA lesions, including bulky lesions induced by platinum-based chemotherapeutic agents. Expression levels of NER factors and resistance to chemotherapy has been examined with some suggestion that NER plays a role in tumour resistance; however, there is a great degree of variability in these studies. Nevertheless, recent clinical studies have suggested Xeroderma Pigmentosum group A (XPA) protein, a key regulator of the NER pathway that is essential for the repair of DNA damage induced by platinum-based chemotherapeutics, as a potential prognostic and predictive biomarker for response to treatment. XPA functions in damage verification step in NER, as well as a molecular scaffold to assemble other NER core factors around the DNA damage site, mediated by protein–protein interactions. In this review, we focus on the interacting partners and mechanisms of regulation of the XPA protein. We summarize clinical oncology data related to this DNA repair factor, particularly its relationship with treatment outcome, and examine the potential of XPA as a target for small molecule inhibitors.

• XPA protein
• biomarker
• cancer
• nucleotide excision repair
• prognostic and predictive value
• single nucleotide polymorphism
• small molecule inhibitors

• 1-NM-PP1
• CTD
• RNA polymerase II
• RNA processing
• TPR
• XPC
• analog-sensitive CTD kinase
• mESC undifferentiated state
• mRNA nuclear export
• nuclear pore
• transcription

• NT2 cell
• bone morphogenetic protein-2 (BMP-2)
• cancer stem cells
• cell differentiation
• differentiation
• genome stability
• muscle cell
• neuron
• nucleotide excision repair
• retinoic acid (RA)
• stem cell
• transcriptomics
• vascular smooth muscle cells

The DNA damage sensor XPC is involved in nucleotide excision repair. Here we show that in the absence of damage, XPC co-localizes with RNA polymerase II (Pol II) and active post-translational histone modifications marks on a subset of class II promoters in human fibroblasts. XPC depletion triggers specific gene down-expression due to a drop in the deposition of histone H3K9 acetylation mark and pre-initiation complex formation. XPC interacts with the histone acetyltransferase KAT2A and specifically triggers the recruitment of the KAT2A-containing ATAC complex to the promoters of down-expressed genes. We show that a strong E2F1 signature characterizes the XPC/KAT2A-bound promoters and that XPC interacts with E2F1 and promotes its binding to its DNA element. Our data reveal that the DNA repair factor XPC is also an RNA polymerase II cofactor recruiting the ATAC coactivator complex to promoters by interacting with the DNA binding transcription factor E2F1.

XPC plays an important role in the nuclear exicision repair pathways. Here the authors show that in addition, XPC plays a role in transcription regulation by interacting with KAT2A and E2F1 and recruiting the ATAC coactivator complex to promoters.

Type II germ cell cancers (GCC) are divided into seminomas, which are highly similar to primordial germ cells and embryonal carcinomas (EC), often described as malignant counterparts to embryonic stem cells.

Previously, we demonstrated that the development of GCCs is a highly plastic process and strongly influenced by the microenvironment. While orthotopic transplantation into the testis promotes seminomatous growth of the seminoma-like cell line TCam-2, ectopic xenotransplantation into the flank initiates reprogramming into an EC-like fate.

During this reprogramming, BMP signaling is inhibited, leading to induction of NODAL signaling, upregulation of pluripotency factors and downregulation of seminoma markers, like SOX17. The pluripotency factor and EC-marker SOX2 is strongly induced.

Here, we adressed the molecular role of SOX2 in this reprogramming. Using CRISPR/Cas9-mediated genome-editing, we established SOX2-deficient TCam-2 cells. Xenografting of SOX2-deficient cells into the flank of nude mice resulted in maintenance of a seminoma-like fate, indicated by the histology and expression of OCT3/4, SOX17, TFAP2C, PRDM1 and PRAME. In SOX2-deficient cells, BMP signaling is inhibited, but NODAL signaling is not activated. Thus, SOX2 appears to be downstream of BMP signaling but upstream of NODAL activation. So, SOX2 is an essential factor in acquiring an EC-like cell fate from seminomas.

A small population of differentiated cells was identified resembling a mixed non-seminoma. Analyses of these cells revealed downregulation of the pluripotency and seminoma markers OCT3/4, SOX17, PRDM1 and TFAP2C. In contrast, the pioneer factor FOXA2 and its target genes were upregulated, suggesting that FOXA2 might play an important role in induction of non-seminomatous differentiation.

• SOX2/SOX17
• TCam-2
• embryonal carcinoma
• reprogramming
• seminoma

In this study, Ho et al. research the mechanism by which TDG-dependent DNA demethylation occurs in a rapid and site-specific manner. Their findings demonstrate two distinct but complementary mechanisms by which XPC influences gene regulation by coordinating efficient TDG-mediated DNA demethylation along with active transcription during somatic cell reprogramming.

Faithful resetting of the epigenetic memory of a somatic cell to a pluripotent state during cellular reprogramming requires DNA methylation to silence somatic gene expression and dynamic DNA demethylation to activate pluripotency gene transcription. The removal of methylated cytosines requires the base excision repair enzyme TDG, but the mechanism by which TDG-dependent DNA demethylation occurs in a rapid and site-specific manner remains unclear. Here we show that the XPC DNA repair complex is a potent accelerator of global and locus-specific DNA demethylation in somatic and pluripotent stem cells. XPC cooperates with TDG genome-wide to stimulate the turnover of essential intermediates by overcoming slow TDG–abasic product dissociation during active DNA demethylation. We further establish that DNA demethylation induced by XPC expression in somatic cells overcomes an early epigenetic barrier in cellular reprogramming and facilitates the generation of more robust induced pluripotent stem cells, characterized by enhanced pluripotency-associated gene expression and self-renewal capacity. Taken together with our previous studies establishing the XPC complex as a transcriptional coactivator, our findings underscore two distinct but complementary mechanisms by which XPC influences gene regulation by coordinating efficient TDG-mediated DNA demethylation along with active transcription during somatic cell reprogramming.

• DNA methylation
• epigenetics
• pluripotency
• reprogramming

• DNA damage
• DNA repair
• Nucleotide excision repair
• Nucleus
• Transcription

• Cancer stem cells
• Circulating tumor cells
• Disseminated tumor cells
• Epithelial-mesenchymal transition
• Metastasis-initiating cells
• Metastatic niche

7,12-Dimethylbenz(a)anthracene (DMBA) rapidly suppresses hematopoietic progenitors, measured as colony forming units (CFU), in mouse bone marrow (BM) leading to mature cell losses as replenishment fails. These losses are mediated by Cyp1b1, independent of the AhR, despite induction of Cyp1b1. BM mesenchymal progenitor cells (MPC) may mediate these responses since basal Cyp1b1 is minimally induced. PreB colony forming unit activity (PreB CFU) is lost within 24 hours in isolated BM cells (BMC) unless cocultured with cells derived from primary MPC (BMS2 line). The mouse embryonic OP9 line, which provides more efficient coculture support, shares similar induction-resistant Cyp1b1 characteristics. This OP9 support is suppressed by DMBA, which is then prevented by Cyp1b1 inhibitors. OP9-enriched medium partially sustains CFU activities but loses DMBA-mediated suppression, consistent with mediation by OP9 Cyp1b1. PreB CFU activity in BMC from Cyp1b1-ko mice has enhanced sensitivity to DMBA. BMC gene expression profiles identified cytokines and developmental factors that are substantially changed in Cyp1b1-ko mice. DMBA had few effects in WT mice but systematically modified many clustered responses in Cyp1b1-ko mice. Typical BMC AhR-responsive genes were insensitive to Cyp1b1 deletion. TCDD replicated Cyp1b1 interventions, suggesting alternative AhR mediation. Cyp1b1 also diminishes oxidative stress, a key cause of stem cell instability.

• DNA repair
• UV radiation
• aging
• cyclobutane pyrimidine dimer
• genomic instability
• photoproducts
• skin cancer
• sunburns

Xeroderma pigmentosum (XP) is a group of genetic disorders caused by mutations of XP-associated genes, resulting in impairment of DNA repair. XP patients frequently exhibit neurological degeneration, but the underlying mechanism is unknown, in part due to lack of proper disease models. Here, we generated patient-specific induced pluripotent stem cells (iPSCs) harboring mutations in five different XP genes including XPA, XPB, XPC, XPG, and XPV. These iPSCs were further differentiated to neural cells, and their susceptibility to DNA damage stress was investigated. Mutation of XPA in either neural stem cells (NSCs) or neurons resulted in severe DNA damage repair defects, and these neural cells with mutant XPA were hyper-sensitive to DNA damage-induced apoptosis. Thus, XP-mutant neural cells represent valuable tools to clarify the molecular mechanisms of neurological abnormalities in the XP patients.

• disease model
• iPSC
• neural stem cell
• neuron
• xeroderma pigmentosum

• Aging
• DNA repair
• Diurnal life
• Genomic instability
• SUMO
• Skin cancer
• Sunburn
• Tumor suppressor
• Ubiquitin

• Animals
• DNA Adducts
• DNA Damage
• DNA Repair/genetics
• DNA-Binding Proteins/chemistry
• DNA-Binding Proteins/genetics
• DNA-Binding Proteins/physiology
• Genomic Instability
• Humans
• Mice
• Models, Genetic
• Models, Molecular
• Protein Structure, Tertiary
• Skin Neoplasms/genetics
• Ultraviolet Rays

• Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)
• Krebsliga Schweiz (CH)
• Velux Stiftung (CH)
• National Science Foundation (US)

Transient DNA strand break formation has been identified as an effective means to enhance gene expression in living cells. In the muscle lineage, cell differentiation is contingent upon the induction of caspase-mediated DNA strand breaks, which act to establish the terminal gene expression program. This coordinated DNA nicking is rapidly resolved, suggesting that myoblasts may deploy DNA repair machinery to stabilize the genome and entrench the differentiated phenotype. Here, we identify the base excision repair pathway component XRCC1 as an indispensable mediator of muscle differentiation. Caspase-triggered XRCC1 repair foci form rapidly within differentiating myonuclei, and then dissipate as the maturation program proceeds. Skeletal myoblast deletion of Xrcc1 does not have an impact on cell growth, yet leads to perinatal lethality, with sustained DNA damage and impaired myofiber development. Together, these results demonstrate that XRCC1 manages a temporally responsive DNA repair process to advance the muscle differentiation program.

• DNA strand breaks
• XRCC1
• base excision repair
• muscle differentiation

• DNA repair
• biochemistry
• stem cells
• structure
• transcription

• BER
• DNA repair
• GG-NER
• Nucleotide excision repair
• Rad4
• XPC