scholarly journals Chromatin modifiers alter recombination between divergent DNA sequences

2019 ◽  
Author(s):  
Ujani Chakraborty ◽  
Beata Mackenroth ◽  
David Shalloway ◽  
Eric Alani
Keyword(s):  
Mismatch Repair ◽  
Histone Deacetylase ◽  
Dna Sequences ◽  
Dna Lesions ◽  
Chromatin Conformation ◽  
Histone Chaperones ◽  
Epigenetic Factors ◽  
Protein Levels ◽  
Dna Substrates ◽  
Heteroduplex Rejection

AbstractRecombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In baker’s yeast such anti-recombination mechanisms can be initiated by the recognition of DNA mismatches in heteroduplex DNA by MSH proteins, followed by recruitment of the Sgs1-Top3-Rmi1 helicase-topoisomerase complex to unwind the recombination intermediate. We previously showed that the repair/rejection decision during single-strand annealing recombination is temporally regulated by MSH protein levels and by factors that excise non-homologous single-stranded tails. These observations, coupled with recent studies indicating that mismatch repair factors interact with components of the histone chaperone machinery, encouraged us to explore roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. This work involved the use of an inverted repeat recombination assay thought to measure sister chromatid repair during DNA replication. Our observations are consistent with the histone chaperones CAF-1 and Rtt106 and the histone deacetylase Sir2 acting to suppress heteroduplex rejection and the Rpd3, Hst3 and Hst4 deacetylases acting to promote heteroduplex rejection. These observations and double mutant analysis have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with mismatch repair factors that mediate heteroduplex rejection.SummaryRecombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In this study we explored roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. Our observations are consistent with the histone chaperones CAF-1 and Rtt106 and the histone deacetylase Sir2 acting to suppress heteroduplex rejection and the Rpd3, Hst3 and Hst4 deacetylases acting to promote heteroduplex rejection. These observations have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with mismatch repair factors that mediate heteroduplex rejection.

scholarly journals The Conversion Gradient at HIS4 of Saccharomyces cerevisiae. I. Heteroduplex Rejection and Restoration of Mendelian Segregation

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 555-572 ◽  
Author(s):  
Kenneth J Hillers ◽  
Franklin W Stahl
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mismatch Repair ◽  
Dna Double Strand Breaks ◽  
Mendelian Segregation ◽  
Strand Breaks ◽  
Conversion Model ◽  
Repair Enzymes ◽  
Heteroduplex Rejection ◽  
Aberrant Segregation ◽  
Hybrid Dna

Abstract In Saccharomyces cerevisiae, some gene loci manifest gradients in the frequency of aberrant segregation in meiosis, with the high end of each gradient corresponding to a hotspot for DNA double-strand breaks (DSBs). The slope of a gradient is reduced when mismatch repair functions fail to act upon heteroduplex DNA—aberrant segregation frequencies at the low end of the gradient are higher in the absence of mismatch repair. Two models for the role of mismatch repair functions in the generation of meiotic “conversion gradients” have been proposed. The heteroduplex rejection model suggests that recognition of mismatches by mismatch repair enzymes limits hybrid DNA flanking the site of a DSB. The restoration-conversion model proposes that mismatch repair does not affect the length of hybrid DNA, but instead increasingly favors restoration of Mendelian segregation over full conversion with increasing distance from the DSB site. In our experiment designed to distinguish between these two models, data for one subset of well repairable mismatches in the HIS4 gene failed to show restoration-type repair but did indicate reduction in the length of hybrid DNA, supporting the heteroduplex rejection model. However, another subset of data manifested restoration-type repair, indicating a relationship between Holliday junction resolution and mismatch repair. We also present evidence for the infrequent formation of symmetric hybrid DNA during meiotic DSB repair.

scholarly journals Regulation of Histone Deacetylase 4 Expression by the SP Family of Transcription Factors

2006 ◽  
Vol 17 (2) ◽  
pp. 585-597 ◽  
Author(s):  
Fang Liu ◽  
Nabendu Pore ◽  
Mijin Kim ◽  
K. Ranh Voong ◽  
Melissa Dowling ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Sequences ◽  
Chromatin Immunoprecipitation ◽  
Histone Deacetylases ◽  
Targeted Mutagenesis ◽  
Cellular Functions ◽  
Specific Expression ◽  
Protein Levels ◽  
Histone Deacetylase 4 ◽  
First Time

Histone deacetylases mediate critical cellular functions but relatively little is known about mechanisms controlling their expression, including expression of HDAC4, a class II HDAC implicated in the modulation of cellular differentiation and viability. Endogenous HDAC4 mRNA, protein levels and promoter activity were all readily repressed by mithramycin, suggesting regulation by GC-rich DNA sequences. We validated consensus binding sites for Sp1/Sp3 transcription factors in the HDAC4 promoter through truncation studies and targeted mutagenesis. Specific and functional binding by Sp1/Sp3 at these sites was confirmed with chromatin immunoprecipitation (ChIP) and electromobility shift assays (EMSA). Cotransfection of either Sp1 or Sp3 with a reporter driven by the HDAC4 promoter led to high activities in SL2 insect cells (which lack endogenous Sp1/Sp3). In human cells, restored expression of Sp1 and Sp3 up-regulated HDAC4 protein levels, whereas levels were decreased by RNA-interference-mediated knockdown of either protein. Finally, variable levels of Sp1 were in concordance with that of HDAC4 in a number of human tissues and cancer cell lines. These studies together characterize for the first time the activity of the HDAC4 promoter, through which Sp1 and Sp3 modulates expression of HDAC4 and which may contribute to tissue or cell-line-specific expression of HDAC4.

Dysregulation of X-Ray Repair Cross Complementing 4 Expression in the Eutopic Endometrium of Women with Endometriosis

Reproduction ◽  
2022 ◽  
Author(s):  
Kashmira Bane ◽  
Junita Desouza ◽  
Asma Rojewale ◽  
Rajendra Katkam ◽  
Gwendolyn Fernandes ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Damage ◽  
Critical Role ◽  
Dna Lesions ◽  
Dna Breaks ◽  
Eutopic Endometrium ◽  
Nhej Pathway ◽  
X Ray ◽  
Protein Levels ◽  
Ishikawa Cells

Recent data suggest that the DNA damage response (DDR) is altered in the eutopic endometrium (EE) of women with endometriosis and this probably ensues in response to higher DNA damage encountered by the EE in endometriosis. DDR operates in a tissue-specific manner and involves different pathways depending on the type of DNA lesions. Among these pathways, the non-homologous end joining (NHEJ) pathway plays a critical role in the repair of double-stranded DNA breaks. The present study was undertaken to explore whether NHEJ is affected in the EE of women with endometriosis. Towards this, we focused on the X-Ray Repair Cross-Complementing 4 (XRCC4) protein, one of the core components of the NHEJ pathway. Endometrial XRCC4 protein levels in the mid-proliferative phase were found significantly (p<0.05) downregulated in women with endometriosis, compared to control women. Investigation of a microarray-based largest dataset in the GEO database (GSE51981) revealed a similar trend at the transcript level in the EE of women with endometriosis, compared to control women. Further in-vitro studies were undertaken to explore the effects of H2O2-induced oxidative stress on DNA damage, as assessed by γ-H2AFX and 8-hydroxy-2’-deoxyguanosine (8-OHdG) immunolocalization, and XRCC4 protein levels in endometrial stromal (ThESCs) and epithelial (Ishikawa) cells. A significant decrease in XRCC4 protein levels and significantly higher localization of γ-H2AFX and 8-OHdG were evident in ThESCs and Ishikawa cells experiencing oxidative stress. Overall, the study demonstrates that the endometrial XRCC4 expression is dysregulated in women with endometriosis and this could be due to higher oxidative stress in endometriosis.

scholarly journals Mismatch Repair, But Not Heteroduplex Rejection, Is Temporally Coupled to DNA Replication

Science ◽  
2011 ◽  
Vol 334 (6063) ◽  
pp. 1713-1716 ◽  
Author(s):  
H. Hombauer ◽  
A. Srivatsan ◽  
C. D. Putnam ◽  
R. D. Kolodner
Keyword(s):  
Dna Replication ◽  
Mismatch Repair ◽  
Heteroduplex Rejection

scholarly journals DNA interstrand cross-links promote chromosomal integration of a selected gene in human cells.

1989 ◽  
Vol 9 (7) ◽  
pp. 2897-2905 ◽  
Author(s):  
J M Vos ◽  
P C Hanawalt
Keyword(s):  
Dna Sequences ◽  
Plasmid Dna ◽  
Simian Virus 40 ◽  
Transcription Unit ◽  
Dna Lesions ◽  
Cross Linking ◽  
Chromosomal Integration ◽  
Nonhomologous Recombination ◽  
Interstrand Cross Links ◽  
Cross Links

We have used integrative pSV2 plasmids to learn how DNA lesions affect nonhomologous recombination with human chromosomes. Enhanced stable transformation of fibrosarcoma cells with a selectable gene was observed after chemical modification of the plasmid DNA; thus, cells transfected with plasmid pSV2-gpt carrying photoadducts of the cross-linking agent 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) yielded four- to sevenfold-higher levels of Gpt+ transformants than were obtained with untreated plasmid. The enhancement due to HMT interstrand cross-links was at least as great as that due to the monoadducts. DNA hybridization analysis indicated that the enhanced transformation frequency resulted from an increased number of cells carrying integrated plasmid sequences rather than from a higher copy number per transformant. The enhancement was not seen with a plasmid missing the sequences flanking the minimal simian virus 40 gpt transcription unit. Cotransfection with untreated and HMT-treated plasmids suggested that the HMT-containing DNA interacted preferentially with some cellular factor that promoted chromosomal integration of the plasmid DNA. It is concluded that (i) interstrand cross-linking as well as intrastrand DNA adducts promote nonhomologous recombination in human chromatin and (ii) DNA sequences flanking the selectable genes are the targets for such recombinational events.

Quantitative Proteomic Analysis Implicates An Altered B-Cell Differentiation State as a Mechanism Underlying GC-Resistance in An Acute Lymphoblastic Leukaemia (ALL) Cell Line Model.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1736-1736
Author(s):  
Lindsay Nicholson ◽  
Caroline Evans ◽  
Elizabeth Matheson ◽  
Lynne Minto ◽  
Christopher Keilty ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Acute Lymphoblastic Leukaemia ◽  
B Cell ◽  
Cell Line ◽  
Mismatch Repair ◽  
Cell Lines ◽  
Lymphoblastic Leukaemia ◽  
B Cell Differentiation ◽  
Protein Levels ◽  
Resistant Phenotype

Abstract Abstract 1736 Poster Board I-762 Introduction Glucocorticoids (GC) are pivotal agents used in the treatment of childhood acute lymphoblastic leukaemia (ALL). GC-resistance is a significant prognostic indicator of a poor treatment outcome in childhood ALL, but the underlying molecular basis remains unclear. Previous studies using cell lines have identified mutation/deletion of the glucocorticoid receptor (GR) as a mechanism of GC-resistance. However, genetic aberration of the GR is rare in clinical samples1. This disparity may be due to the mismatch repair deficient status of many ALL cell lines which consequently have a greater likelihood of acquiring mutations under GC-selection. We have used a discovery proteomics approach for hypothesis generation on potential mechanisms for resistance. To achieve this, we compared a well-characterized mismatch repair proficient GC-sensitive cell line, PreB 697, and a GC-resistant sub-clone (R3F9) both bearing wildtype GR, in a comparative proteomics experiment using 4-channel isobaric tagging for relative and absolute quantitation (the iTRAQ approach). Methods Cells were treated with either vehicle control or 0.1μM dexamethasone for 24 hours and subjected to subcellular fractionation to prepare a nuclear fraction. Each sample was labelled with a distinct isobaric tag for relative quantification and analysed by 2-dimensional liquid chromatography/ tandem mass spectrometry. The proteins were identified and relatively quantified using Protein Pilot software (Applied Biosystems). Ratios were calculated for dexamethasone-treated ‘versus’ control vehicle for each cell line and an ITRAQ ratio of greater than or equal to ± 1.2 or less than 0.8 fold change were considered to be differentially expressed. Results The comparative dataset highlighted two transcription factors which are involved in B-cell differentiation, PAX5 and IRF4, to be differentially expressed in the PreB 697 compared to the R3F9 cell line. The GC-resistant R3F9 cell line had reduced PAX5 and IRF4 protein expression compared to the parental cell line and this was further validated in other GC-resistant sub-clones derived from the PreB 697 cell line by western blot analysis. The reduced PAX5 level in the GC-resistant cell lines was not due to monoallelic loss, as measured by a QRT-PCR method or mutation as determined by DHPLC analysis of ‘hot-spot’ exons. In addition, PAX5 mRNA levels were not significantly altered, thus suggestive of a post-transcriptional mechanism for PAX5 protein reduction. To test the direct role of PAX5 in GC-resistance, we reduced PAX5 mRNA and protein levels using RNA interference in the parental GC-sensitive, PreB 697 cell line. PAX5 protein levels were reduced by at least 80% and were maintained for 48 hours post-transfection. The PreB 697 cell line was transfected with siRNA directed to PAX5 using electroporation, the cells were allowed to recover for 24 hours and the levels of cell kill were assessed in response to a 48 hour incubation with 1 μM dexamethasone by Annexin V staining and the MTS assay. Paradoxically, PAX5 knockdown increased GC-sensitivity (mean 60.4% apoptosis, S.D. 16.8, N=3) in comparison to a non-specific siRNA (mean 31.0% apoptosis, S.D. 5.2, N=3) but did not influence sensitivity to either vincristine or daunorubicin. Thus, this response was specific to glucocorticoids. Conclusion Using a proteomic approach we have shown alterations in PAX5 protein levels are associated with a GC-resistant phenotype which an mRNA-based technology would fail to detect. Modulation of PAX5 in ALL cells may influence the response to GC-therapy. It is known that GC-sensitivity alters during B-cell development, with early lymphoid precursors being highly sensitive and more mature B cells being highly resistant to GC-induced apoptosis. We propose that reduced PAX5 protein levels may reflect an altered differentiation state of the sub-clones of PreB 697 which are associated with a GC resistant phenotype. 1Irving et al, Cancer Res, 2005 2Schmidt et al, FASEB, 2006 Disclosures No relevant conflicts of interest to declare.

scholarly journals Histone Deacetylase 10 Regulates DNA Mismatch Repair and May Involve the Deacetylation of MutS Homolog 2

2015 ◽  
Vol 290 (37) ◽  
pp. 22795-22804 ◽  
Author(s):  
Rangasudhagar Radhakrishnan ◽  
Yixuan Li ◽  
Shengyan Xiang ◽  
Fenghua Yuan ◽  
Zhigang Yuan ◽  
...  
Keyword(s):  
Mismatch Repair ◽  
Histone Deacetylase ◽  
Dna Mismatch Repair ◽  
Dna Mismatch

scholarly journals The reactions of the EcoRi and other restriction endonucleases

1979 ◽  
Vol 179 (2) ◽  
pp. 353-365 ◽  
Author(s):  
S E Halford ◽  
N P Johnson ◽  
J Grinsted
Keyword(s):  
Restriction Endonuclease ◽  
Dna Sequences ◽  
Recognition Site ◽  
Single Strand ◽  
Restriction Endonucleases ◽  
Dna Duplex ◽  
Phosphodiester Bond ◽  
Linear Dna ◽  
Ecori Restriction ◽  
Dna Substrates

The reaction of the EcoRI restriction endonuclease was studied with both the plasmid pMB9 and DNA from bacteriophage lambda as the substrates. With both circular and linear DNA molecules, the only reaction catalysed by the EcoRI restriction endonuclease was the hydrolysis of the phosphodiester bond within one strand of the recognition site on the DNA duplex. The cleavage of both strands of the duplex was achieved only after two independent reactions, each involving a single-strand scission. The reactivity of the enzyme for single-strand scissions was the same for both the first and the second cleavage within its recognition site. No differences were observed between the mechanism of action on supercoiled and linear DNA substrates. Other restriction endonucleases were tested against plasmid pMB9. The HindIII restriction endonuclease cleaved DNA in the same manner as the EcoRI enzyme. However, in contrast with EcoRI, the Sa/I and the BamHI restriction endonucleases appeared to cleave both strands of the DNA duplex almost simultaneously. The function of symmetrical DNA sequences and the conformation of the DNA involved in these DNA–protein interactions are discussed in the light of these observations. The fact that the same reactions were observed on both supercoiled and linear DNA substrates implies that these interactions do not involve the unwinding of the duplex before catalysis.

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