An analytical pipeline for genomic representations used for cytosine methylation studies

Thompson, Reid F.; Reimers, Mark; Khulan, Batbayar; Gissot, Mathieu; Richmond, Todd; Chen, Quan; Zheng, Xin; Kim, Kami; Greally, John M.

doi:10.1093/bioinformatics/btn096

Cited by 50 publications

(63 citation statements)

References 32 publications

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“…44 This genomic methylation array of 720,001 probes was designed to focus on CpG islands near transcription start sites. The Pearson Correlation test 45 showed that the majority of methylation intensity signals was similar in all cell lines (Fig. S2A).…”

Section: Dna Demethylating Agent 5-aza-deoxycytidine (5-aza-dc) Revermentioning

confidence: 95%

RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

Mei

Brenner

2014

Cell Cycle

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Site-specific hypermethylation of tumor suppressor genes accompanied by genome-wide hypomethylation are epigenetic hallmarks of malignancy. However, the molecular mechanisms that drive these linked changes in DNA methylation remain obscure. DNA methyltransferase 1 (DNMT1), the principle enzyme responsible for maintaining methylation patterns is commonly dysregulated in tumors. Replication foci targeting sequence (RFTS) is an N-terminal domain of DNMT1 that inhibits DNA-binding and catalytic activity, suggesting that RFTS deletion would result in a gain of DNMT1 function. However, a substantial body of data suggested that RFTS is required for DNMT1 activity. Here, we demonstrate that deletion of RFTS alters DNMT1-dependent DNA methylation during malignant transformation. Compared to full-length DNMT1, ectopic expression of hyperactive DNMT1-DRFTS caused greater malignant transformation and enhanced promoter methylation with condensed chromatin structure that silenced DAPK and DUOX1 expression. Simultaneously, deletion of RFTS impaired DNMT1 chromatin association with pericentromeric Satellite 2 (SAT2) repeat sequences and produced DNA demethylation at SAT2 repeats and globally. To our knowledge, RFTS-deleted DNMT1 is the first single factor that can reprogram focal hypermethylation and global hypomethylation in parallel during malignant transformation. Our evidence suggests that the RFTS domain of DNMT1 is a target responsible for epigenetic changes in cancer.

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Section: Dna Demethylating Agent 5-aza-deoxycytidine (5-aza-dc) Revermentioning

confidence: 95%

RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

Mei

Brenner

2014

Cell Cycle

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“…Freshly isolated islets were used for all studies. To remove the confounding factors contributed by even slight differences in purity between islet preparations, we use quantitative RT-PCR to determine the relative levels of endocrine (insulin) and exocrine (amylase) gene expression levels in each sample as previously described (15). This approach allowed us to determine that there was negligible exocrine tissue contamination of isolated pancreatic islets.…”

Section: Methodsmentioning

confidence: 99%

“…Microarray Data Analysis-Microarray data were pre-processed and subject to quality control and quantile normalization as we have previously described (15). HpaII/MspI ratio values were then compared between groups for all loci throughout the rat genome using a standard t test for IUGR (n ϭ 4) and controls (n ϭ 4).…”

Section: Methodsmentioning

confidence: 99%

“…Rats-We performed a whole genome cytosine methylation assay on pancreatic islets isolated at 7 weeks from SpragueDawley rats in each of two groups: IUGR offspring (n ϭ 4) and their sham-operated controls (n ϭ 4), and confirmed overall data quality for each sample as previously described (15). To detect global patterns of epigenomic change distinguishing IUGR and control animals, we compared one thousand randomly selected loci to generate a representative heat map.…”

Section: Distinct Patterns Of Dna Methylation In Iugr and Controlmentioning

confidence: 99%

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Experimental Intrauterine Growth Restriction Induces Alterations in DNA Methylation and Gene Expression in Pancreatic Islets of Rats

Thompson

Fazzari

Niu

et al. 2010

Journal of Biological Chemistry

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143

119

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Intrauterine growth restriction (IUGR) increases susceptibility to age-related diseases, including type 2 diabetes (T2DM), and is associated with permanent and progressive changes in gene expression. Our study was designed to test whether epigenomic dysregulation mediates the cellular memory of this intrauterine event. To test this hypothesis, we isolated pancreatic islets from control and IUGR (induced by bilateral uterine artery ligation at day 18 of fetal life) animals at 7 weeks of age. Using the HELP (HpaII tiny fragment enrichment by ligationmediated PCR) assay, we generated the first DNA methylation map at almost 1 million unique sites throughout the rat genome in normal pancreatic islet cells, allowing us to identify the changes that occur as a consequence of IUGR. We validated candidate dysregulated loci with quantitative assays of cytosine methylation and gene expression. IUGR changes cytosine methylation at ϳ1,400 loci (false discovery rate of 4.2%) in male rats at 7 weeks of age, preceding the development of diabetes and thus representing candidate loci for mediating the pathogenesis of metabolic disease that occurs later in life. Epigenetic dysregulation occurred preferentially at conserved intergenic sequences, frequently near genes regulating processes known to be abnormal in IUGR islets, such as vascularization, ␤-cell proliferation, insulin secretion, and cell death, associated with concordant changes in mRNA expression. These results demonstrate that epigenetic dysregulation is a strong candidate for propagating the cellular memory of intrauterine events, causing changes in expression of nearby genes and long term susceptibility to type 2 diabetes.Perturbations in the intrauterine environment resulting in poor fetal growth increase the susceptibility for age-related diseases, particularly type 2 diabetes mellitus (T2DM) 4 and cardiovascular disease (1, 2). Moreover, intrauterine growth restriction (IUGR) can cause permanent and progressive changes in gene expression, affecting important metabolically active tissues such as pancreatic islets (3-6). These changes are often present at birth or during early life, and can precede the development of overt disease in rodents by months and in humans by decades. Although the mechanisms that may mediate the "fetal origin of adult disease" (7) remain unclear, dysregulation of the epigenome could play an important role and may explain the changes in gene expression that are heritably maintained through cell divisions in IUGR animals throughout life (8).We have developed an animal model of IUGR caused by uteroplacental insufficiency, which limits the supply of critical substrates (e.g. nutrients, oxygen, growth factors, and hormones) to the fetus (9). This deficient intrauterine environment affects fetal development through permanent and progressive dysregulation of gene expression and function of susceptible cells (e.g. pancreatic ␤-cells) and leads to the development of T2DM in adulthood (3, 6, 9). In particular, expression of pancreatic and duodenal home...

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“…A 720K Roche-NimbleGen custom array capturing 117 521 HpaII fragments was used to assay CpG islands, CpG island shores and reference sequence promoters. Quality control of arrays included assessment of MspI and HpaII intensity distribution and spatial uniformity of the Cy3 and Cy5 signals (49). For all queried HpaII fragments, intensities were processed to determine the Q-centered (Qcent) ratio and the log 2 multi-sample, quantile-normalized unmethylated/methylated (HpaII/MspI) ratio.…”

Section: Help Assaymentioning

confidence: 99%

Cigarette smoking induces small airway epithelial epigenetic changes with corresponding modulation of gene expression

Buro-Auriemma

Salit

Hackett

et al. 2013

Human Molecular Genetics

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The small airway epithelium (SAE), the first site of smoking-induced lung pathology, exhibits genome-wide changes in gene expression in response to cigarette smoking. Based on the increasing evidence that the epigenome can respond to external stimuli in a rapid manner, we assessed the SAE of smokers for genome-wide DNA methylation changes compared with nonsmokers, and whether changes in SAE DNA methylation were linked to the transcriptional output of these cells. Using genome-wide methylation analysis of SAE DNA of nonsmokers and smokers, the data identified 204 unique genes differentially methylated in SAE DNA of smokers compared with nonsmokers, with 67% of the regions with differential methylation occurring within 2 kb of the transcriptional start site. Among the genes with differential methylation were those related to metabolism, transcription, signal transduction and transport. For the differentially methylated genes, 35 exhibited a correlation with gene expression, 54% with an inverse correlation of DNA methylation with gene expression and 46% a direct correlation. These observations provide evidence that cigarette smoking alters the DNA methylation patterning of the SAE and that, for some genes, these changes are associated with the smoking-related changes in gene expression.

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An analytical pipeline for genomic representations used for cytosine methylation studies

Cited by 50 publications

References 32 publications

RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

Experimental Intrauterine Growth Restriction Induces Alterations in DNA Methylation and Gene Expression in Pancreatic Islets of Rats

Cigarette smoking induces small airway epithelial epigenetic changes with corresponding modulation of gene expression

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