scholarly journals SIRT1 gene expression upon genotoxic damage is regulated by APE1 through nCaRE-promoter elements

2014 ◽  
Vol 25 (4) ◽  
pp. 532-547 ◽  
Author(s):  
Giulia Antoniali ◽  
Lisa Lirussi ◽  
Chiara D'Ambrosio ◽  
Fabrizio Dal Piaz ◽  
Carlo Vascotto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Stability ◽  
Gene Expression Regulation ◽  
Excision Repair ◽  
Genotoxic Stress ◽  
Early Response ◽  
Dna Lesions ◽  
Sirtuin 1 ◽  
Gene Promoters ◽  
Sirt1 Gene

Apurinic/apyrimidinic endonuclease 1 (APE1) is a multifunctional protein contributing to genome stability via repair of DNA lesions via the base excision repair pathway. It also plays a role in gene expression regulation and RNA metabolism. Another, poorly characterized function is its ability to bind to negative calcium responsive elements (nCaRE) of some gene promoters. The presence of many functional nCaRE sequences regulating gene transcription can be envisioned, given their conservation within ALU repeats. To look for functional nCaRE sequences within the human genome, we performed bioinformatic analyses and identified 57 genes potentially regulated by APE1. We focused on sirtuin-1 (SIRT1) deacetylase due to its involvement in cell stress, including senescence, apoptosis, and tumorigenesis, and its role in the deacetylation of APE1 after genotoxic stress. The human SIRT1 promoter presents two nCaRE elements stably bound by APE1 through its N-terminus. We demonstrate that APE1 is part of a multiprotein complex including hOGG1, Ku70, and RNA Pol II, which is recruited on SIRT1 promoter to regulate SIRT1 gene functions during early response to oxidative stress. These findings provide new insights into the role of nCaRE sequences in the transcriptional regulation of mammalian genes.

scholarly journals Nucleolar accumulation of APE1 depends on charged lysine residues that undergo acetylation upon genotoxic stress and modulate its BER activity in cells

2012 ◽  
Vol 23 (20) ◽  
pp. 4079-4096 ◽  
Author(s):  
Lisa Lirussi ◽  
Giulia Antoniali ◽  
Carlo Vascotto ◽  
Chiara D'Ambrosio ◽  
Mattia Poletto ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Mammalian Cells ◽  
Excision Repair ◽  
Genotoxic Stress ◽  
Dna Lesions ◽  
Sirtuin 1 ◽  
Genotoxic Damage ◽  
Base Excision

Apurinic/apyrimidinic endonuclease 1 (APE1) is the main abasic endonuclease in the base excision repair (BER) pathway of DNA lesions caused by oxidation/alkylation in mammalian cells; within nucleoli it interacts with nucleophosmin and rRNA through N-terminal Lys residues, some of which (K27/K31/K32/K35) may undergo acetylation in vivo. Here we study the functional role of these modifications during genotoxic damage and their in vivo relevance. We demonstrate that cells expressing a specific K-to-A multiple mutant are APE1 nucleolar deficient and are more resistant to genotoxic treatment than those expressing the wild type, although they show impaired proliferation. Of interest, we find that genotoxic treatment induces acetylation at these K residues. We also find that the charged status of K27/K31/K32/K35 modulates acetylation at K6/K7 residues that are known to be involved in the coordination of BER activity through a mechanism regulated by the sirtuin 1 deacetylase. Of note, structural studies show that acetylation at K27/K31/K32/K35 may account for local conformational changes on APE1 protein structure. These results highlight the emerging role of acetylation of critical Lys residues in regulating APE1 functions. They also suggest the existence of cross-talk between different Lys residues of APE1 occurring upon genotoxic damage, which may modulate APE1 subnuclear distribution and enzymatic activity in vivo.

scholarly journals Stress Marks on the Genome: Use or Lose?

2019 ◽  
Vol 20 (2) ◽  
pp. 364 ◽  
Author(s):  
Bayan Bokhari ◽  
Sudha Sharma
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Genome Stability ◽  
Cellular Responses ◽  
Dna Lesions ◽  
Gene Promoters ◽  
Physiological Processes ◽  
Base Modifications ◽  
Gene Expression Alterations ◽  
Transcription And Replication

Oxidative stress and the resulting damage to DNA are inevitable consequence of endogenous physiological processes further amplified by cellular responses to environmental exposures. If left unrepaired, oxidative DNA lesions can block essential processes such as transcription and replication or can induce mutations. Emerging data also indicate that oxidative base modifications such as 8-oxoG in gene promoters may serve as epigenetic marks, and/or provide a platform for coordination of the initial steps of DNA repair and the assembly of the transcriptional machinery to launch adequate gene expression alterations. Here, we briefly review the current understanding of oxidative lesions in genome stability maintenance and regulation of basal and inducible transcription.

scholarly journals Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Nicola P. Montaldo ◽  
Diana L. Bordin ◽  
Alessandro Brambilla ◽  
Marcel Rösinger ◽  
Sarah L. Fordyce Martin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Stability ◽  
Genome Instability ◽  
Excision Repair ◽  
Regulation Of Gene Expression ◽  
Direct Interaction ◽  
Dna Glycosylase ◽  
Pol Ii ◽  
Naked Dna ◽  
Alkyladenine Dna Glycosylase

AbstractBase excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases, including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here, we show that AAG binds to chromatin and forms complex with RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes, aberrantly methylated bases accumulate towards the 3′end in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide insights into genome stability maintenance in actively transcribing chromatin and reveal roles of aberrantly methylated bases in regulation of gene expression.

scholarly journals Kinetochores Prevent Repair of UV Damage in Saccharomyces cerevisiae Centromeres

2004 ◽  
Vol 24 (16) ◽  
pp. 6907-6918 ◽  
Author(s):  
Christoph Capiaghi ◽  
The Vinh Ho ◽  
Fritz Thoma
Keyword(s):  
Genome Stability ◽  
Excision Repair ◽  
Dna Lesions ◽  
Uv Damage ◽  
Dna Interactions ◽  
Centromere Proteins ◽  
Protein Dna Interactions ◽  
Nucleotide Excision ◽  
Repair Pathways ◽  
Segregation Of Chromosomes

ABSTRACT Centromeres form specialized chromatin structures termed kinetochores which are required for accurate segregation of chromosomes. DNA lesions might disrupt protein-DNA interactions, thereby compromising segregation and genome stability. We show that yeast centromeres are heavily resistant to removal of UV-induced DNA lesions by two different repair systems, photolyase and nucleotide excision repair. Repair resistance persists in G1- and G2/M-arrested cells. Efficient repair was obtained only by disruption of the kinetochore structure in a ndc10-1 mutant, but not in cse4-1 and cbf1Δ mutants. Moreover, UV photofootprinting and DNA repair footprinting showed that centromere proteins cover about 120 bp of the centromere elements CDEII and CDEIII, including 20 bp of flanking CDEIII. Thus, DNA lesions do not appear to disrupt protein-DNA interactions in the centromere. Maintaining a stable kinetochore structure seems to be more important for the cell than immediate removal of DNA lesions. It is conceivable that centromeres are repaired by postreplication repair pathways.

scholarly journals Small-Activating RNA Can Change Nucleosome Positioning in Human Fibroblasts

2016 ◽  
Vol 21 (6) ◽  
pp. 634-642 ◽  
Author(s):  
Bin Wang ◽  
Jing Sun ◽  
Jiandong Shi ◽  
Qing Guo ◽  
Xiangrong Tong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Gene Expression Regulation ◽  
Human Fibroblasts ◽  
Cpg Islands ◽  
Nucleosome Positioning ◽  
Gene Promoters ◽  
Promoter Regions ◽  
Rna Activation ◽  
Gene Expression Studies

RNA activation (RNAa) is a mechanism of positive gene expression regulation mediated by small-activating RNAs (saRNAs), which target gene promoters and have been used as tools to manipulate gene expression. Studies have shown that RNAa is associated with epigenetic modifications at promoter regions; however, it is unclear whether these modifications are the cause or a consequence of RNAa. In this study, we examined changes in nucleosome repositioning and the involvement of RNA polymerase II (RNAPII) in this process. We screened saRNAs for OCT4 ( POU5F1), SOX2, and NANOG, and identified several novel saRNAs. We found that nucleosome positioning was altered after saRNA treatment and that the formation of nucleosome-depleted regions (NDRs) contributed to RNAa at sites of RNAPII binding, such as the TATA box, CpG islands (CGIs), proximal enhancers, and proximal promoters. Moreover, RNAPII appeared to be bound specifically to NDRs. These results suggested that changes in nucleosome positions resulted from RNAa. We thus propose a hypothesis that targeting promoter regions using exogenous saRNAs can induce the formation of NDRs, exposing regulatory binding sites to recruit RNAPII, a key component of preinitiation complex, and leading to increased initiation of transcription.

scholarly journals Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress

2022 ◽  
Vol 119 (3) ◽  
pp. e2105898119
Author(s):  
Yiji Liao ◽  
Chen-Hao Chen ◽  
Tengfei Xiao ◽  
Bárbara de la Peña Avalos ◽  
Eloise V. Dray ◽  
...  
Keyword(s):  
Gene Expression ◽  
Solid Tumors ◽  
Excision Repair ◽  
Genotoxic Stress ◽  
Inhibitory Effect ◽  
Cancer Therapies ◽  
Transactivation Domain ◽  
Castration Resistant Prostate Cancer ◽  
Public Data ◽  
Mechanistic Basis

Drugs that block the activity of the methyltransferase EZH2 are in clinical development for the treatment of non-Hodgkin lymphomas harboring EZH2 gain-of-function mutations that enhance its polycomb repressive function. We have previously reported that EZH2 can act as a transcriptional activator in castration-resistant prostate cancer (CRPC). Now we show that EZH2 inhibitors can also block the transactivation activity of EZH2 and inhibit the growth of CRPC cells. Gene expression and epigenomics profiling of cells treated with EZH2 inhibitors demonstrated that in addition to derepressing gene expression, these compounds also robustly down-regulate a set of DNA damage repair (DDR) genes, especially those involved in the base excision repair (BER) pathway. Methylation of the pioneer factor FOXA1 by EZH2 contributes to the activation of these genes, and interaction with the transcriptional coactivator P300 via the transactivation domain on EZH2 directly turns on the transcription. In addition, CRISPR-Cas9–mediated knockout screens in the presence of EZH2 inhibitors identified these BER genes as the determinants that underlie the growth-inhibitory effect of EZH2 inhibitors. Interrogation of public data from diverse types of solid tumors expressing wild-type EZH2 demonstrated that expression of DDR genes is significantly correlated with EZH2 dependency and cellular sensitivity to EZH2 inhibitors. Consistent with these findings, treatment of CRPC cells with EZH2 inhibitors dramatically enhances their sensitivity to genotoxic stress. These studies reveal a previously unappreciated mechanism of action of EZH2 inhibitors and provide a mechanistic basis for potential combination cancer therapies.

scholarly journals “Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression”

2019 ◽  
Author(s):  
Nicola P. Montaldo ◽  
Diana L. Bordin ◽  
Alessandro Brambilla ◽  
Marcel Rösinger ◽  
Sarah L. Fordyce Martin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Stability ◽  
Genome Instability ◽  
Excision Repair ◽  
Regulation Of Gene Expression ◽  
Direct Interaction ◽  
Dna Glycosylase ◽  
Pol Ii ◽  
Naked Dna ◽  
Alkyladenine Dna Glycosylase

AbstractBase excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG; aka MPG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here we show that AAG binds to chromatin and forms complex with active RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes aberrantly methylated bases accumulate towards 3’end, in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide novel insights to maintaining genome stability in actively transcribing chromatin, and reveal roles of aberrantly methylated bases in regulation of gene expression.

scholarly journals DDB1 Maintains Genome Integrity through Regulation of Cdt1

2006 ◽  
Vol 26 (21) ◽  
pp. 7977-7990 ◽  
Author(s):  
Courtney A. Lovejoy ◽  
Kimberli Lock ◽  
Ashwini Yenamandra ◽  
David Cortez
Keyword(s):  
Dna Damage ◽  
Genome Stability ◽  
Genome Instability ◽  
Excision Repair ◽  
Dna Lesions ◽  
Cell Cycle Checkpoints ◽  
Dna Double Strand Breaks ◽  
Genome Maintenance ◽  
Strand Breaks ◽  
Ubiquitin Ligase Complex

ABSTRACT DDB1, a component of a Cul4A ubiquitin ligase complex, promotes nucleotide excision repair (NER) and regulates DNA replication. We have investigated the role of human DDB1 in maintaining genome stability. DDB1-depleted cells accumulate DNA double-strand breaks in widely dispersed regions throughout the genome and have activated ATM and ATR cell cycle checkpoints. Depletion of Cul4A yields similar phenotypes, indicating that an E3 ligase function of DDB1 is important for genome maintenance. In contrast, depletion of DDB2, XPA, or XPC does not cause activation of DNA damage checkpoints, indicating that defects in NER are not involved. One substrate of DDB1-Cul4A that is crucial for preventing genome instability is Cdt1. DDB1-depleted cells exhibit increased levels of Cdt1 protein and rereplication, despite containing other Cdt1 regulatory mechanisms. The rereplication, accumulation of DNA damage, and activation of checkpoint responses in DDB1-depleted cells require entry into S phase and are partially, but not completely, suppressed by codepletion of Cdt1. Therefore, DDB1 prevents DNA lesions from accumulating in replicating human cells, in part by regulating Cdt1 degradation.

scholarly journals ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xi Chen ◽  
Xu Shi ◽  
Andrew F. Neuwald ◽  
Leena Hilakivi-Clarke ◽  
Robert Clarke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Large Scale ◽  
Target Genes ◽  
Gene Expression Regulation ◽  
Software Tool ◽  
Gene Promoters ◽  
Weak Binding ◽  
Genomic Locations ◽  
And Control

Abstract Background ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak binding sites, especially those at promoters and enhancers, are functionally important because they also regulate nearby gene expression. Yet, it remains a challenge to accurately identify weak binding sites in ChIP-seq data due to the ambiguity in differentiating these weak binding sites from the amplified background DNAs. Results ChIP-BIT2 (http://sourceforge.net/projects/chipbitc/) is a software package for ChIP-seq peak detection. ChIP-BIT2 employs a mixture model integrating protein and control ChIP-seq data and predicts strong or weak protein binding sites at promoters, enhancers, or other genomic locations. For binding sites at gene promoters, ChIP-BIT2 simultaneously predicts their target genes. ChIP-BIT2 has been validated on benchmark regions and tested using large-scale ENCODE ChIP-seq data, demonstrating its high accuracy and wide applicability. Conclusion ChIP-BIT2 is an efficient ChIP-seq peak caller. It provides a better lens to examine weak binding sites and can refine or extend the existing binding site collection, providing additional regulatory regions for decoding the mechanism of gene expression regulation.

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