Role of CTCF in DNA damage response

Tanwar, Vinay Singh; Jose, Cynthia C.; Cuddapah, Suresh

doi:10.1016/j.mrrev.2018.02.002

Cited by 23 publications

(16 citation statements)

References 120 publications

(212 reference statements)

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“…ATF-4 is induced by translation under hypoxic conditions and mediates part of the unfolded protein response after ER stress ( Köditz et al, 2007 ). CTCF is a highly conserved, ubiquitous zinc finger protein, and it is related to many important cellular processes, such as transcription activation, repression, insulation, imprinting, and promotion of DNA double-strand break repair ( Tanwar et al, 2019 ).…”

Section: Resultsmentioning

confidence: 99%

Genetic Variants and Functional Analyses of the ATG16L1 Gene Promoter in Acute Myocardial Infarction

et al. 2021

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BackgroundAcute myocardial infarction (AMI), a common complex disease caused by an interaction between genetic and environmental factors, is a serious type of coronary artery disease and is also a leading cause of death worldwide. Autophagy-related 16-like 1 (ATG16L1) is a key regulatory factor of autophagy and plays an important role in induced autophagy. In the cardiovascular system, autophagy is essential to preserve the homeostasis and function of the heart and blood vessels. No studies have hitherto examined the association between AMI and ATG16L1 gene promoter.MethodsWe conducted a case-control study, using polymerase chain reaction and sequencing techniques, dual luciferase reporter assay, and electrophoretic mobility shift assay, to analyze genetic and functional variation in the ATG16L1 gene promoter between AMI and controls. A variety of statistical analyses were used to analyze the allele and genotype frequencies and the relationship between single-nucleotide polymorphisms (SNPs) and AMI.ResultsIn all, 10 SNPs and two DNA-sequence variants (DSVs) were identified in 688 subjects, and three ATG16L1 gene promoter mutations [g.233250693 T > C (rs185213911), g.233250946 G > A (rs568956599), g.233251133 C > G (rs1301744254)] that were identified in AMI patients significantly altered the transcriptional activity of ATG16L1 gene promoter in HEH2, HEK-293, and H9c2 cells (P < 0.05). Further electrophoretic mobility shift assays indicated that the SNPs affected the binding of transcription factors (P < 0.01).ConclusionATG16L1 gene promoter mutations in AMI patients may affect the binding of transcription factors and change the transcriptional activity of the ATG16L1 gene, changing the level of autophagy and contributing to the occurrence and development of AMI as rare and low-frequency risk factors.

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Section: Resultsmentioning

confidence: 99%

Genetic Variants and Functional Analyses of the ATG16L1 Gene Promoter in Acute Myocardial Infarction

et al. 2021

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“…However, it should be taken into account that the IDLV off-target detection is less efficient than other methods, such as GUIDE-seq and Digenome-seq [ 46 , 47 ]. The inclusion of the IS2 element may recruit several proteins, including multifunctional proteins such as the CCCTC-binding factor (CTCF), which facilitate the integration of IDLVs into the DSBs, thus probably increasing sensitivity to DSB strapping [ 48 , 49 , 50 ]. We experimentally assessed whether the inclusion of IS2 enhances the capacity of SE-IDLVs to integrate into DSBs, thereby increasing the potential of IDLVs to act as off-target sensors.…”

Section: Resultsmentioning

confidence: 99%

Improved Functionality of Integration-Deficient Lentiviral Vectors (IDLVs) by the Inclusion of IS2 Protein Docks

et al. 2021

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Integration-deficient lentiviral vectors (IDLVs) have recently generated increasing interest, not only as a tool for transient gene delivery, but also as a technique for detecting off-target cleavage in gene-editing methodologies which rely on customized endonucleases (ENs). Despite their broad potential applications, the efficacy of IDLVs has historically been limited by low transgene expression and by the reduced sensitivity to detect low-frequency off-target events. We have previously reported that the incorporation of the chimeric sequence element IS2 into the long terminal repeat (LTR) of IDLVs increases gene expression levels, while also reducing the episome yield inside transduced cells. Our study demonstrates that the effectiveness of IDLVs relies on the balance between two parameters which can be modulated by the inclusion of IS2 sequences. In the present study, we explore new IDLV configurations harboring several elements based on IS2 modifications engineered to mediate more efficient transgene expression without affecting the targeted cell load. Of all the insulators and configurations analysed, the insertion of the IS2 into the 3′LTR produced the best results. After demonstrating a DAPI-low nuclear gene repositioning of IS2-containing episomes, we determined whether, in addition to a positive effect on transcription, the IS2 could improve the capture of IDLVs on double strand breaks (DSBs). Thus, DSBs were randomly generated, using the etoposide or locus-specific CRISPR-Cas9. Our results show that the IS2 element improved the efficacy of IDLV DSB detection. Altogether, our data indicate that the insertion of IS2 into the LTR of IDLVs improved, not only their transgene expression levels, but also their ability to be inserted into existing DSBs. This could have significant implications for the development of an unbiased detection tool for off-target cleavage sites from different specific nucleases.

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“…Taken together, previous reports and our data highlight the significance of post-translational modifications in controlling the stability and stress-responsiveness of CTCF in a cell-type and context-dependent manner. Another important consideration is the likely adverse impact of environmental toxins on the diverse functions of CTCF and how this might contribute to impaired biological processes and degenerative diseases [ 32 ].…”

Section: Discussionmentioning

confidence: 99%

“…Recent studies have defined critical roles for CTCF in the cellular stress response [32] and the importance of post-translational modifications that are known to affect CTCF activity, most notably poly(ADP-ribosylation) (PARylation) [80], phosphorylation [81], and SUMOylation [82] (diagrammed in S3 Fig) . One study showed that upon genotoxic damage in cancer PLOS GENETICS cell lines, CTCF is rapidly recruited to DNA damage sites via interaction of zinc finger DNA binding motifs with poly (ADP-ribose) (PAR) moieties [83]. This report also showed that CTCF-deficient human osteosarcoma U2OS cells rendered them hypersensitive to genotoxic stress.…”

Section: Discussionmentioning

confidence: 99%

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Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress

et al. 2021

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The nuclear protein CCCTC-binding factor (CTCF) has diverse roles in chromatin architecture and gene regulation. Functionally, CTCF associates with thousands of genomic sites and interacts with proteins, such as cohesin, or non-coding RNAs to facilitate specific transcriptional programming. In this study, we examined CTCF during the cellular stress response in human primary cells using immune-blotting, quantitative real time-PCR, chromatin immunoprecipitation-sequence (ChIP-seq) analysis, mass spectrometry, RNA immunoprecipitation-sequence analysis (RIP-seq), and Airyscan confocal microscopy. Unexpectedly, we found that CTCF is exquisitely sensitive to diverse forms of stress in normal patient-derived human mammary epithelial cells (HMECs). In HMECs, a subset of CTCF protein forms complexes that localize to Serine/arginine-rich splicing factor (SC-35)-containing nuclear speckles. Upon stress, this species of CTCF protein is rapidly downregulated by changes in protein stability, resulting in loss of CTCF from SC-35 nuclear speckles and changes in CTCF-RNA interactions. Our ChIP-seq analysis indicated that CTCF binding to genomic DNA is largely unchanged. Restoration of the stress-sensitive pool of CTCF protein abundance and re-localization to nuclear speckles can be achieved by inhibition of proteasome-mediated degradation. Surprisingly, we observed the same characteristics of the stress response during neuronal differentiation of human pluripotent stem cells (hPSCs). CTCF forms stress-sensitive complexes that localize to SC-35 nuclear speckles during a specific stage of neuronal commitment/development but not in differentiated neurons. We speculate that these particular CTCF complexes serve a role in RNA processing that may be intimately linked with specific genes in the vicinity of nuclear speckles, potentially to maintain cells in a certain differentiation state, that is dynamically regulated by environmental signals. The stress-regulated activity of CTCF is uncoupled in persistently stressed, epigenetically re-programmed “variant” HMECs and certain cancer cell lines. These results reveal new insights into CTCF function in cell differentiation and the stress-response with implications for oxidative damage-induced cancer initiation and neuro-degenerative diseases.

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Role of CTCF in DNA damage response

Cited by 23 publications

References 120 publications

Genetic Variants and Functional Analyses of the ATG16L1 Gene Promoter in Acute Myocardial Infarction

Genetic Variants and Functional Analyses of the ATG16L1 Gene Promoter in Acute Myocardial Infarction

Improved Functionality of Integration-Deficient Lentiviral Vectors (IDLVs) by the Inclusion of IS2 Protein Docks

Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress

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