2-Aminopurine as a probe for mismatch repair in mammalian cells and its relationship to DNA methylation

Mutagenesis ◽  
1989 ◽  
Vol 4 (4) ◽  
pp. 302-305
Author(s):  
W. P. Diver ◽  
D. M. Woodcock
Keyword(s):  
Dna Methylation ◽  
Mismatch Repair ◽  
Mammalian Cells

scholarly journals Use of a Small Palindrome Genetic Marker to Investigate Mechanisms of Double-Strand-Break Repair in Mammalian Cells

Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 1281-1289 ◽  
Author(s):  
Julang Li ◽  
Mark D Baker
Keyword(s):  
Mismatch Repair ◽  
Mammalian Cells ◽  
Indirect Evidence ◽  
Strand Break ◽  
Double Strand Break ◽  
Double Strand Break Repair ◽  
Chromosomal Markers ◽  
Vector Borne ◽  
Break Repair ◽  
The One

Abstract We examined mechanisms of mammalian homologous recombination using a gene targeting assay in which the vector-borne region of homology to the chromosome bore small palindrome insertions that frequently escape mismatch repair when encompassed within heteroduplex DNA (hDNA). Our assay permitted the product(s) of each independent recombination event to be recovered for molecular analysis. The results revealed the following: (i) vector-borne double-strand break (DSB) processing usually did not yield a large double-strand gap (DSG); (ii) in 43% of the recombinants, the results were consistent with crossover at or near the DSB; and (iii) in the remaining recombinants, hDNA was an intermediate. The sectored (mixed) genotypes observed in 38% of the recombinants provided direct evidence for involvement of hDNA, while indirect evidence was obtained from the patterns of mismatch repair (MMR). Individual hDNA tracts were either long or short and asymmetric or symmetric on the one side of the DSB examined. Clonal analysis of the sectored recombinants revealed how vector-borne and chromosomal markers were linked in each strand of individual hDNA intermediates. As expected, vector-borne and chromosomal markers usually resided on opposite strands. However, in one recombinant, they were linked on the same strand. The results are discussed with particular reference to the double-strand-break repair (DSBR) model of recombination.

Mismatch repair of heteroduplex DNA intermediates of extrachromosomal recombination in mammalian cells

1994 ◽  
Vol 14 (1) ◽  
pp. 400-406
Author(s):  
W P Deng ◽  
J A Nickoloff
Keyword(s):  
Dna Replication ◽  
Mismatch Repair ◽  
Mammalian Cells ◽  
Strand Break ◽  
Wild Type ◽  
Heteroduplex Dna ◽  
Frameshift Mutations ◽  
Single Strand Annealing ◽  
Extrachromosomal Recombination ◽  
Strand Annealing

Previous work indicated that extrachromosomal recombination in mammalian cells could be explained by the single-strand annealing (SSA) model. This model predicts that extrachromosomal recombination leads to nonconservative crossover products and that heteroduplex DNA (hDNA) is formed by annealing of complementary single strands. Mismatched bases in hDNA may subsequently be repaired to wild-type or mutant sequences, or they may remain unrepaired and segregate following DNA replication. We describe a system to examine the formation and mismatch repair of hDNA in recombination intermediates. Our results are consistent with extrachromosomal recombination occurring via SSA and producing crossover recombinant products. As predicted by the SSA model, hDNA was present in double-strand break-induced recombination intermediates. By placing either silent or frameshift mutations in the predicted hDNA region, we have shown that mismatches are efficiently repaired prior to DNA replication.

scholarly journals HGG-20. DNA METHYLATION ANALYSIS OF HIGH-GRADE GLIOMA IN PATIENTS WITH MISMATCH REPAIR DEFICIENCIES

2018 ◽  
Vol 20 (suppl_2) ◽  
pp. i92-i93
Author(s):  
Andrew Dodgshun ◽  
Kohei Fukuoka ◽  
Brittany Campbell ◽  
Melissa Edwards ◽  
Alexandra Sexton-Oates ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mismatch Repair ◽  
High Grade Glioma ◽  
High Grade ◽  
Methylation Analysis ◽  
Dna Methylation Analysis

scholarly journals Control of the DNA Methylation System Component MBD2 by Protein Arginine Methylation

2006 ◽  
Vol 26 (19) ◽  
pp. 7224-7235 ◽  
Author(s):  
Choon Ping Tan ◽  
Sara Nakielny
Keyword(s):  
Dna Methylation ◽  
Complex Formation ◽  
Histone Deacetylases ◽  
Mammalian Cells ◽  
Genome Stability ◽  
Epigenetic Modification ◽  
Arginine Methylation ◽  
System Component ◽  
Transcription Repression ◽  
Mbd Proteins

ABSTRACT DNA methylation is vital for proper chromatin structure and function in mammalian cells. Genetic removal of the enzymes that catalyze DNA methylation results in defective imprinting, transposon silencing, X chromosome dosage compensation, and genome stability. This epigenetic modification is interpreted by methyl-DNA binding domain (MBD) proteins. MBD proteins respond to methylated DNA by recruiting histone deacetylases (HDAC) and other transcription repression factors to the chromatin. The MBD2 protein is dispensable for animal viability, but it is implicated in the genesis of colon tumors. Here we report that the MBD2 protein is controlled by arginine methylation. We identify the protein arginine methyltransferase enzymes that catalyze this modification and show that arginine methylation inhibits the function of MBD2. Arginine methylation of MBD2 reduces MBD2-methyl-DNA complex formation, reduces MBD2-HDAC repression complex formation, and impairs the transcription repression function of MBD2 in cells. Our report provides a molecular description of a potential regulatory mechanism for an MBD protein family member. It is the first to demonstrate that protein arginine methyltransferases participate in the DNA methylation system of chromatin control.

scholarly journals DNA methylation directs microRNA biogenesis in mammalian cells

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Ohad Glaich ◽  
Shivang Parikh ◽  
Rachel E. Bell ◽  
Keren Mekahel ◽  
Maya Donyo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Mammalian Cells ◽  
Sequence Conservation ◽  
Mirna Biogenesis ◽  
Coding Sequence ◽  
Microrna Biogenesis ◽  
Flanking Regions

AbstractMicroRNA (miRNA) biogenesis initiates co-transcriptionally, but how the Microprocessor machinery pinpoints the locations of short precursor miRNA sequences within long flanking regions of the transcript is not known. Here we show that miRNA biogenesis depends on DNA methylation. When the regions flanking the miRNA coding sequence are highly methylated, the miRNAs are more highly expressed, have greater sequence conservation, and are more likely to drive cancer-related phenotypes than miRNAs encoded by unmethylated loci. We show that the removal of DNA methylation from miRNA loci leads to their downregulation. Further, we found that MeCP2 binding to methylated miRNA loci halts RNA polymerase II elongation, leading to enhanced processing of the primary miRNA by Drosha. Taken together, our data reveal that DNA methylation directly affects miRNA biogenesis.

Methylation Profile of B-Chronic Lymphocytic Leukemia Cells.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2951-2951
Author(s):  
Jun Fan ◽  
Asou Norio ◽  
Masao Matsuoka
Keyword(s):  
Dna Methylation ◽  
Chronic Lymphocytic Leukemia ◽  
Cell Lines ◽  
Mammalian Cells ◽  
Mononuclear Cells ◽  
Cpg Island ◽  
Methylation Status ◽  
Lymphocytic Leukemia ◽  
Dna Hypomethylation ◽  
Peripheral Blood Mononuclear

Abstract DNA methylation plays an important role in the development and aging of mammalian cells, and its dysregulation has been frequently observed in cancer cells. The purpose of this study is to investigate the involvement of aberrant DNA methylation in B chronic lymphocytic leukemia (B-CLL) cells. We compared methylation status of B-CLL cells isolated from patients with that of normal CD19+ cells isolated from health donors by methylated CpG island amplification/representative difference analysis method. 5 hypermethylated and 27 hypomethylated DNA regions were identified in B-CLL sample. Among the 27 hypomethylated regions, 5 located on chromosome 9q34, 3 on 10q25-26 and 4 on 19q13. Methylation status was confirmed by sequencing using sodium bisulfite-treated DNA samples. By comparing DNA samples from same patients at different clinical stages, we found that lower methylation density in these regions is linked with disease progression. Expression of 15 genes surrounding hypomethylated regions was studied by RT-PCR. Expression of laminin beta3 gene and melanotransferrin gene was found to be upregulated in all B-CLL cell lines as well as lymphoma cell lines comparing with normal CD19+ peripheral blood mononuclear cells. B-cell CLL/lymphoma 11b gene showed increased expression in only 2 B-CLL cell lines. For other genes, no transcriptional change was found regardless of changed DNA methylation. This study showed the predominance of DNA hypomethylation in B-CLL cells compared with hypermethylation. Hypomethylated regions clustered in a limited number of chromosomes and methylation density appeared to be inversely correlated with disease progress. Figure Figure

scholarly journals HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples

2015 ◽  
Vol 14s2 ◽  
pp. CIN.S17286 ◽  
Author(s):  
Shuying Sun ◽  
Peng Li
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Mammalian Cells ◽  
Single Sample ◽  
Methyl Group ◽  
Genome Wide ◽  
Two Samples ◽  
Clustering Patterns

DNA methylation (the addition of a methyl group to a cytosine) is an important epigenetic event in mammalian cells because it plays a key role in regulating gene expression. Most previous methylation studies assume that DNA methylation occurs on both positive and negative strands. However, a few studies have reported that in some genes, methylation occurs only on one strand (ie, hemimethylation) and has clustering patterns. These studies report that hemimethylation occurs on individual genes. It is unclear whether hemimethylation occurs genome-wide and whether there are hemimethylation differences between cancerous and noncancerous cells. To address these questions, we have developed the first-ever pipeline, named hemimethylation pipeline (HMPL), to identify hemimethylation patterns. Utilizing the available software and the newly developed Perl and R scripts, HMPL can identify hemimethylation patterns for a single sample and can also compare two different samples.

Delayed DNA methylation is an integral feature of DNA replication in mammalian cells

1986 ◽  
Vol 166 (1) ◽  
pp. 103-112 ◽  
Author(s):  
D.M. Woodcock ◽  
D.L. Simmons ◽  
P.J. Crowther ◽  
I.A. Cooper ◽  
K.J. Trainor ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Replication ◽  
Mammalian Cells ◽  
Integral Feature
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