scholarly journals Acetylation of UHRF1 Regulates Hemi-methylated DNA Binding and Maintenance of Genome-wide DNA Methylation

Cell Reports ◽  
2020 ◽  
Vol 32 (4) ◽  
pp. 107958
Author(s):  
Ja Young Hahm ◽  
Jin Woo Park ◽  
Joo-Young Kang ◽  
Junyoung Park ◽  
Chul-Hong Kim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Methylated Dna ◽  
Genome Wide

scholarly journals The major histocompatibility complex class II promoter-binding protein RFX (NF-X) is a methylated DNA-binding protein.

1993 ◽  
Vol 13 (11) ◽  
pp. 6810-6818 ◽  
Author(s):  
X Y Zhang ◽  
N Jabrane-Ferrat ◽  
C K Asiedu ◽  
S Samac ◽  
B M Peterlin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Dna Sequences ◽  
Protein Complexes ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Class Ii ◽  
Major Histocompatibility ◽  
Methylated Dna ◽  
Mammalian Protein

A mammalian protein called RFX or NF-X binds to the X box (or X1 box) in the promoters of a number of major histocompatibility (MHC) class II genes. In this study, RFX was shown to have the same DNA-binding specificity as methylated DNA-binding protein (MDBP), and its own cDNA was found to contain a binding site for MDBP in the leader region. MDBP is a ubiquitous mammalian protein that binds to certain DNA sequences preferentially when they are CpG methylated and to other related sequences, like the X box, irrespective of DNA methylation. MDBP from HeLa and Raji cells formed DNA-protein complexes with X-box oligonucleotides that coelectrophoresed with those containing standard MDBP sites. Furthermore, MDBP and X-box oligonucleotides cross-competed for the formation of these DNA-protein complexes. DNA-protein complexes obtained with MDBP sites displayed the same partial supershifting with an antiserum directed to the N terminus of RFX seen for complexes containing an X-box oligonucleotide. Also, the in vitro-transcribed-translated product of a recombinant RFX cDNA bound specifically to MDBP ligands and displayed the DNA methylation-dependent binding of MDBP. RFX therefore contains MDBP activity and thereby also EF-C, EP, and MIF activities that are indistinguishable from MDBP and that bind to methylation-independent sites in the transcriptional enhancers of polyomavirus and hepatitis B virus and to an intron of c-myc.

scholarly journals Effect of site-specific DNA methylation and mutagenesis on recognition by methylated DNA-binding protein from human placenta

1986 ◽  
Vol 14 (21) ◽  
pp. 8387-8397 ◽  
Author(s):  
Xian-Yang Zhang ◽  
Kenneth C. Ehrlich ◽  
Richard Y.-H. Wang ◽  
Melanie Ehrlich
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Human Placenta ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Site Specific ◽  
Methylated Dna

scholarly journals Genome-wide DNA methylation profiles of porcine ovaries in estrus and proestrus

2018 ◽  
Vol 50 (9) ◽  
pp. 714-723 ◽  
Author(s):  
Xiaolong Zhou ◽  
Songbai Yang ◽  
Feifei Yan ◽  
Ke He ◽  
Ayong Zhao
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Cpg Islands ◽  
Biological Processes ◽  
Hormone Regulation ◽  
Methylated Dna ◽  
Coding Regions ◽  
Genome Wide ◽  
Differentially Methylated Genes ◽  
Flanking Regions

DNA methylation is an important epigenetic modification involved in the estrous cycle and the regulation of reproduction. Here, we investigated the genome-wide profiles of DNA methylation in porcine ovaries in proestrus and estrus using methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in intergenic and intron regions. The methylation levels of coding regions were higher than those of the 5′- and 3′-flanking regions of genes. There were 4,813 differentially methylated regions (DMRs) of CpG islands in the estrus vs. proestrus ovarian genomes. Additionally, 3,651 differentially methylated genes (DMGs) were identified in pigs in estrus and proestrus. The DMGs were significantly enriched in biological processes and pathways related to reproduction and hormone regulation. We identified 90 DMGs associated with regulating reproduction in pigs. Our findings can serve as resources for DNA methylome research focused on porcine ovaries and further our understanding of epigenetically regulated reproduction in mammals.

scholarly journals Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing

Epigenomes ◽  
2017 ◽  
Vol 1 (3) ◽  
pp. 14 ◽  
Author(s):  
Nicklas Staunstrup ◽  
Anna Starnawska ◽  
Mette Nyegaard ◽  
Anders Nielsen ◽  
Anders Børglum ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylated Dna ◽  
Genome Wide ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

Genome-Wide Analysis of DNA Methylation Patterns Reveals Dynamic Epigenetic Regulation of the AML Genome After Decitabine Treatment.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 591-591 ◽  
Author(s):  
Fabienne Brenet ◽  
Michelle Moh ◽  
Patricia Funk ◽  
Daoqui You ◽  
Agnes J. Viale ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Cellular Differentiation ◽  
Transcriptional Activity ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Transcription Start ◽  
Methylated Dna ◽  
Genome Wide ◽  
Methylation Patterns

Abstract Abstract 591 The human genome is adorned with methylated cytosine residues that function in the epigenetic guidance of cellular differentiation and development. Cellular interpretation of this epigenetic mark is incompletely understood and tissue specific patterns of DNA methylation vary with age, can be altered by environmental factors, and are often abnormal in human disease. Aberrant DNA methylation is a common means by which tumor suppressor genes (TSGs) are inactivated during carcinogenesis (Baylin, Herman, Graff, Vertino and Issa 1998; Laird and Jaenisch 1996; Singal and Ginder 1999). Unlike genetic mechanisms of gene inactivation, such as gene deletion and mutation, the epigenetic silencing of TSGs by promoter hypermethylation is potentially reversible. This has led to the broad interest of cancer biologists in the study of DNA methylation. Method: We developed a method for genome-wide analysis of DNA methylation by using a recombinant protein containing a methyl-CpG binding domain (MBD) to enrich methylated DNA fragments that are then identified by massively parallel sequencing using the SOLiD sequencer (ABI). We generated ∼15-million sequence tags per specimen and wrote custom R-language algorithms to develop an analytical platform with which to study DNA methylation. We used this technology to study the pharmacodynamics of DNA methylation in acute myelogenous leukemia (AML) cells following exposure to the hypomethylating agent, 5-aza-2'-deoxycytidine (decitabine). We compared DNA methylation patterns before and after decitabine treatment with transcriptional activity revealed by microarrays (Illumina) and quantitative PCR. We found that Sequence Tag Analysis of Methylation Profiles (STAMP) permits highly reproducible, genome-wide identification of DNA methylation density at near base-pair resolution. This method is cost effective and can be extended, without modification, to any mapped genome. Results: STAMP analysis revealed patterned DNA methylation at all scales across the genome: from whole chromosomes to individual genes. We found that densely methylated elements (DMEs) of the human genome are often highly conserved or closely associated with gene coding regions and promoters. We identified distinct patterns of DNA methylation surrounding the transcription start and termination sites of all genes. These methylation patterns are associated with transcriptional activity of neighboring genes. Interestingly, genes with a densely methylated transcription start site (TSS) have little methylation in the surrounding regions whereas genes with little or no methylation at the TSS have disproportionately higher methylation within their gene bodies. In untreated cells, we detected ∼75,000 DMEs (false discovery rate <0.01) with a median length ∼600 bp and with 75% being less than 960bp. The longest DMEs extend up to ∼24000 bp and are composed of microsatellite clusters. The majority of the DMEs are not classic CpG islands (CGI) but are GC-rich regions (median 57% GC) with a greater than expected incidence of CpG dinucleotides (median CpG observed/expected 0.49): results that suggest the definition of a CGI excludes the majority of the methylated human genome. Although the pattern of DNA methylation was qualitatively similar in cells treated with decitabine, we found that the density of methylation was generally lower and fewer DMEs (∼50,000) were identified. Decitabine treatment led to increased expression of ∼800 genes involved in cell cycle control, apoptosis and cellular differentiation whereas the ∼50 genes with downregulated expression were most commonly involved in RNA metabolism. Distinct pre-treatment DNA methylation patterns were associated with, and tended to predict, the transcriptional activity following treatment with decitabine. Summary: We developed and utilized a powerful new technology to uncover the genome-wide effects of decitabine on DNA methylation patterns in AML. We found that although decitabine induces genome-wide DNA hypomethylation, its effect on transcription depends upon the pattern of DNA methylation prior to treatment. The STAMP methodology leverages the power and flexibility of massively parallel sequencing with the high selectivity of the MBD for its natural ligand, methyl-CpG. This assay permits robust, unbiased and highly sensitive whole-genome identification of methylated DNA segments. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa

2018 ◽  
Vol 69 (1) ◽  
pp. 107 ◽  
Author(s):  
Satoshi Takahashi ◽  
Naoki Fukushima ◽  
Kenji Osabe ◽  
Etsuko Itabashi ◽  
Motoki Shimizu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Brassica Rapa ◽  
Inbred Lines ◽  
Methylated Dna ◽  
Transcriptional Suppression ◽  
Genome Wide ◽  
Transposon Silencing ◽  
Lower Expression ◽  
Model Based Analysis

DNA methylation is an epigenetic gene regulatory mechanism that plays an essential role in gene expression, transposon silencing, genome imprinting and plant development. We investigated the influence of DNA methylation on gene expression in Brassica rapa L., to understand whether epigenetic differences exist between inbred lines. Genome-wide DNA methylation was analysed by methylated DNA immunoprecipitation sequencing (MeDIP-seq) of 14-day-old first and second leaves from two inbred lines of Chinese cabbage, one susceptible and one resistant to fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans. MACS (model-based analysis for ChIP-seq) identified DNA methylation peaks in genic regions including 2 kb upstream, exon, intron and 2 kb downstream. More than 65% of genes showed similar patterns of DNA methylation in the genic regions in the two inbred lines. DNA methylation states of the two inbred lines were compared with their transcriptome. Genes having DNA methylation in the intron and in the 200 bp upstream and downstream regions were associated with a lower expression level in both lines. A small number of genes showed a negative correlation between differences in DNA methylation levels and differences in transcriptional levels in the two inbred lines, suggesting that DNA methylation in these genes results in transcriptional suppression.

Maternal intermittent fasting before mating alters hepatic DNA methylation in offspring

Epigenomics ◽  
2021 ◽  
Author(s):  
Wenzhen Yin ◽  
Yuan Liang ◽  
Lijun Sun ◽  
Yue Yin ◽  
Weizhen Zhang
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Intermittent Fasting ◽  
Global Dna Methylation ◽  
Impaired Glucose Metabolism ◽  
Methylated Dna ◽  
Glucose Levels ◽  
Blood Glucose Levels ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

Aim: Our aim was to explore how maternal intermittent fasting (IF) influences offspring metabolism. Materials & methods: A model of female C57BL/6J mice alternate-day feeding before mating was established and alteration of hepatic DNA methylation in offspring analyzed by whole genome bisulfite sequencing. Results: IF dams weighed less (p = 0.03) and had lower random blood glucose levels (p = 0.04). Lower birth weight (p = 0.0031) and impaired glucose metabolism were also observed in the offspring of the IF mice. The hepatic genome-wide DNA methylation maps showed a correlation between maternal IF and decreased hepatic global DNA methylation of adult offspring. In the offspring liver, 2869 differentially methylated DNA regions were altered. Conclusions: Our finding suggests that maternal IF before mating significantly alters hepatic DNA methylation in offspring.

Genome-Wide DNA Methylation Patterns Reveal Specific Signatures for HSC, CMP and Erythroblasts.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 391-391
Author(s):  
Amber Hogart ◽  
Subramanian S. Ajay ◽  
Hatice Ozel Abaan ◽  
Stacie M. Anderson ◽  
Elliott H. Margulies ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bone Marrow ◽  
Cell Surface ◽  
Gene Silencing ◽  
Blood Cells ◽  
Genomic Dna ◽  
Cell Types ◽  
Methylated Dna ◽  
Genome Wide ◽  
Methylation Patterns

Abstract Abstract 391 DNA methylation is a reversible epigenetic modification that is required for proper mammalian development and is proposed to contribute to the pathogenesis of hematologic diseases including leukemia and bone marrow failure syndromes. Elucidating the pathways and genes regulated by DNA methylation during hematopoiesis may reveal new therapeutic targets for disease. Because the phenotype and activity of hematopoietic stem cells (HSC) and hematopoietic progenitor cells of many different lineages have been defined by both in vitro and in vivo assays, hematopoiesis is an excellent model for investigating epigenomic changes during differentiation. HSCs have the ability to self-renew and to generate blood cells of all lineages, which allows them to repopulate recipients after stem cell transplantation. The common myeloid progenitor (CMP) gives rise to all myeloid cell types including neutrophils, monocytes, platelets, and red blood cells, but cannot self renew or repopulate. In contrast to the multipotent HSC and CMP, erythroblasts (ERY) are terminally committed cells that become mature enucleated red blood cells. These three cell types represent unique stages of lineage commitment with distinct transcriptional programs, and potentially unique epigenomic signatures. In contrast to human HSC, which are defined by the absence of several cell surface markers, mouse HSC have the cell surface phenotype of lineage marker negative (Lin-) c-kit+ Sca-1+ and can be positively selected. For this reason we chose the mouse model for genome-wide methylation profiling. Murine HSC and CMP (Lin- c-kit+ Sca-1-) cells were enriched from adult mouse bone marrow with flow cytometry. Erythroblasts (CD71+/Ter119+) were positively selected from E13.5 mouse fetal livers. Genomic DNA isolated from each enriched cell population was sheared to 200-300 bp fragments. MBD2, one of five endogenous mammalian methyl CpG binding domain proteins, binds methylated DNA sequences with broad affinity. Methylated DNA fragments were enriched from the genomic DNA using a tagged, recombinant MBD2 pulldown kit (Active Motif). After pulldown, enrichment of known methylated sequences regulating the imprints of Snrpn and Rasgrf was validated by qPCR. Two biological replicates of HSC, CMP, and ERY methylated sequences and negative control supernatant fractions were submitted for high-throughput sequencing with the Illumina Genome Analyzer platform. Raw sequence data containing 32-46 × 106 reads of 36-50 base pairs were obtained for each sample. The Eland program was used to map 41-59% of reads to unique sequences in the mouse genome. Model-based Analysis of ChIP-Seq (MACS) was used to estimate the mean and variance of the sequence tag distribution across the genome and define peaks below the significance threshold of p<10-5. The number of methylation peaks decreased as cells differentiated, with 64,000 peaks identified in HSC (24,000 unique), 41,000 peaks in CMP (2000 unique), and 23,000 peaks in ERY (1000 unique). Approximately 20,000 peaks were common between all cell types with 57% of these peaks residing in RefSeq genes, 8% in regions adjacent to RefSeq genes (<10 kb), and 35% of methylation peaks in intergenic regions. Comparison of HSC expression data from Akashi et al (Blood 101: 383, 2003) to our HSC genic methylation peaks revealed that 2/3 of HSC genic peaks are within transcriptionally silent genes while 1/3 of HSC genic peaks are within expressed genes. Although DNA methylation is often associated with gene silencing, the important developmental gene Gata2 contains methylation peaks in HSC and CMP, cells that express Gata2, that are absent in ERY, where Gata2 is repressed. A Gata1-Fog1-Mbd2 complex has been described by Rodriguez et al (EMBO 24: 2354, 2005), therefore providing a link between DNA methylation and proteins known to bind at the Gata2 locus. Grass et al (Mol. Cell. Biol. 26:7056, 2006) determined that Gata2 is regulated by long-range interactions of GATA protein complexes, and consistent with this observation, distinct methylation patterns are observed up to 100 kb upstream of the Gata2 gene. Our genome-wide analysis supports an association of methylation with gene silencing but also suggests that DNA methylation is a dynamic epigenetic mark that influences hematopoietic differentiation. The changes in DNA methylation we observe around Gata2 may also contribute to long-range chromatin organization. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Effects of Antenatal Synthetic Glucocorticoid on Glucocorticoid Receptor Binding, DNA Methylation, and Genome-Wide mRNA Levels in the Fetal Male Hippocampus

Endocrinology ◽  
2013 ◽  
Vol 154 (11) ◽  
pp. 4170-4181 ◽  
Author(s):  
Ariann Crudo ◽  
Sophie Petropoulos ◽  
Matthew Suderman ◽  
Vasilis G. Moisiadis ◽  
Alisa Kostaki ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Fetal Lung ◽  
Late Gestation ◽  
Mrna Levels ◽  
Substantial Impact ◽  
Genome Wide ◽  
Organ Systems ◽  
Endogenous Cortisol

The endogenous glucocorticoid (GC) surge in late gestation plays a vital role in maturation of several organ systems. For this reason, pregnant women at risk of preterm labor are administered synthetic glucocorticoids (sGCs) to promote fetal lung development. Animal studies have shown that fetal sGC exposure can cause life-long changes in endocrine and metabolic function. We have previously shown that antenatal sGC treatment is associated with alterations in global DNA methylation and modifications to the hippocampal methylome and acetylome. In this study, we hypothesized that: 1) there are changes in the transcriptional landscape of the fetal hippocampus in late gestation, associated with the endogenous cortisol surge; 2) fetal sGC exposure alters genome-wide transcription in the hippocampus; and 3) these changes in transcription are associated with modified glucocorticoid receptor (GR) DNA binding and DNA methylation. sGC was administered as 2 courses on gestational days (GD) 40, 41, 50, and 51, and the hippocampi of fetal guinea pigs were examined before (GD52) and after (GD65) the endogenous cortisol surge (Term ∼GD67). We also analyzed fetal hippocampi 24 hours and 14 days following maternal sGC injections (n = 3–4/group). Genome-wide modification of transcription and GR DNA binding occurred in late gestation, in parallel with the normal GC surge. Further, sGC exposure had a substantial impact on the hippocampal transcriptome, GR-DNA binding, and DNA methylation at 24 hours and 14 days following the final sGC treatment. These data support the hypothesis that GC exposure in late gestation plays a significant role in modifying the transcriptional and epigenetic landscape of the developing fetal hippocampus and that substantial effects are evident for at least 2 weeks after sGC exposure.

scholarly journals A novel understanding of global DNA methylation in bobcat (Lynx rufus)

Genome ◽  
2020 ◽  
Vol 63 (2) ◽  
pp. 125-130
Author(s):  
Bonnie Cantrell ◽  
Sydney Friedman ◽  
Hannah Lachance ◽  
Chris Bernier ◽  
Brenda Murdoch ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Conservation Biology ◽  
Differential Methylation ◽  
Lynx Rufus ◽  
Global Dna Methylation ◽  
Epigenetic Mechanisms ◽  
Methylated Dna ◽  
Genome Wide ◽  
Weight Data ◽  
Insight Into

Epigenetic mechanisms may provide a novel prospective of bobcat (Lynx rufus) adaptation to habitat loss/fragmentation. Previous research has focused on bobcat behavior and genetics, but epigenetics has not been studied in bobcat. The aim of this study was to determine the quantity of global DNA methylation in the liver of 30 bobcats. DNA was extracted from liver samples obtained from the Vermont Fish and Wildlife Department. The percent of global DNA methylation was quantified and calculated using the MethylFlashTM Methylated DNA 5-mC Quantification Kit from Epigentek (Farmingdale, NY, USA). Age, sex, and carcass weight data were collected at sampling and analyzed with percent of global DNA methylation. Global DNA methylation was found to range from 0.46% to 2.76%. Age ranged from <1 to 12 years old and weight ranged from 3.18 to 13.61 kg. Further analysis of differential methylation may provide insight into novel means of bobcat conservation within different regions of Vermont. These results reinforce the need for genome-wide epigenetic studies in conservation biology.

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