Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Small RNA mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation

ABSTRACT: Mammalian cells contain copious amounts of RNA including both coding and non-coding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylation targeting and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1) co-purifies with inhibitory ncRNAs. MicroRNAs (miRNAs) binds directly to DNMT1 with high affinity. The binding of miRNAs, such as miR-155, leads to inhibition of DNMT1 enzyme activity. Exogenous miR-155 in cells induces aberrant DNA methylation of the genome, resulting in hypomethylation of low to moderately methylated regions. And small shift of hypermethylation of previously hypomethylated region was also observed. Furthermore, hypomethylation led to activation of genes. Based on these observations, we propose that overexpression of specific miRNAs in human cancer may lead to aberrant DNA methylation and altered gene-expression. Examine of the DNA methylation and mRNA profile of HCT 116 cells transfected by random 23-mer or miR-155 RNA

ORGANISM(S): Homo sapiens

SUBMITTER: Guoqiang Zhang

PROVIDER: E-GEOD-68027 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation.

Zhang Guoqiang G Estève Pierre-Olivier PO Chin Hang Gyeong HG Terragni Jolyon J Dai Nan N Corrêa Ivan R IR Pradhan Sriharsa S

Nucleic acids research 20150518 12

Mammalian cells contain copious amounts of RNA including both coding and noncoding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylation targeting and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1) co-purifies with inhibitory ncRNAs. MicroRNAs (miRNAs) bind directly to DNMT1 with high affinity. The bindi ...[more]

PMID: 25990724

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Project description:The activation-induced cytidine deaminase enzyme (AID) is required in germinal center (GC) B cells for somatic hyper-mutation and class switch recombination at the immunoglobulin locus. In GC-B cells, AID is highly expressed, with inherent mutator activity that helps generate antibody diversity. However, AID may also regulate gene expression epigenetically, irrespective of mutator activity, by directly deaminating 5-methylcytosine (5mC) in concert with base excision repair glycosylases to exchange unmethylated cytosine. This pathway promotes gene demethylation, thereby removing epigenetic memory. For example, AID promotes active demethylation of the genome in primordial germ cells. However, the range and mechanism by which AID promotes pluripotency is not known. Different studies have suggested either a requirement or a lack of function for promoting pluripotency in somatic nuclei following fusion with embryonic stem cells (ESC). Here we tested directly whether AID regulates epigenetic memory, by comparing the relative ability of cells lacking AID to reprogram from a differentiated cell type to an induced pluripotent stem cell (iPSC). We show that loss of AID impacts two distinct steps of reprogramming: First, AID-null cells are transiently hyper-responsive to the reprogramming process. Second, although they initiate expression of pluripotency genes, they fail to stabilize the pluripotent state. The genome of AID-null cells remains hypermethylated in reprogramming cells, and hypermethylated genes associated with pluripotency fail to be stably up-regulated. MYC target genes are highly enriched in the set of genes hypermethylated and under-expressed in reprogramming cells lacking AID. Recent studies identified a distinctive late step of reprogramming associated with methylation status. AID appears to regulate this step to stabilize the pluripotent state, removing epigenetic memory to promote expression of secondary pluripotency network genes. Transcriptome sequencing of AID-null tail fibroblasts, wildtype tail fibroblasts, AID-null and wildtype tail fibroblasts reprogrammed for three weeks by ectopic expression of transcription factors Oct4, Sox2, KLf4 and cMyc. Methylation profiling by reduced representation bisulphite seuencing of AID-null tail fibroblasts, wildtype tail fibroblasts, AID-null and wildtype tail fibroblasts reprogrammed for three weeks and AID-null and wildtype clones after three weeks of reprogramming (Picked at two weeks)

Project description:The samples were collected from the participants of the Finnish Diabetes Prediction and Prevention (DIPP) Study, born between 1995 and 2006. DIPP is a prospective follow-up cohort of children with a moderate or high risk of type 1 diabetes, based on the HLA-DR-DQ genotype. Islet cell autoantibodies (ICA, GADA, IAA, IA2A and ZnT8A) were measured 1 - 4 times per year until age 15 or year 2018. The aim was to study associations between perinatal DNA methylation marks and later progression to type 1 diabetes. Case individuals who became persistently positive for at least two biochemical autoantibodies (GADA, IAA, IA2A or ZnT8A) and/or were diagnosed with type 1 diabetes during the follow-up were compared to the control individuals who remained autoantibody-negative throughout the follow-up. These data were also used in the development of data analysis methodology in bisulfite sequencing studies. To protect the privacy of the study participants, the sequence read data are not publicly available. However, the processed data can be downloaded here. These include two count matrices: \\"methylated_reads\\" and \\"total_reads\\". The matrix \\"methylated_reads\\" contains methylated read counts at each high-coverage CpG site (altogether approximately 2.5 million rows) at each of the 173 samples (173 columns), and the matrix \\"total_reads\\" contains the corresponding total read counts (coverage). Please notice that the methylated read counts are read counts, not percentages. Methylation proportions can be calculated as methylated_reads/total_reads. The row names are the genomic locations of these CpG sites in hg19 (GRCh37) coordinates (1,2). For privacy reasons, all potential SNPs were excluded from these publicly available count matrices. Specifically, we removed all common (minor allele frequency > 1 %) human SNPs, as listed in dbSNP (3). We also removed all SNPs that were detected in one or more samples even with \\"low\\" evidence by BS-SNPer, which is a software for detecting SNPs from bisulfite sequencing data (4). Altogether 204443 out of 2752981 rows were removed from the original coverage-filtered count matrices that were analyzed in the present study. Description of the sample attributes: Individual: The individual-specific identifiers, such as “Subject1”. Since each sample is from a different individual, these correspond to the sample identifiers (Subject1 == Sample 1 etc.) Experimental Group: The variable of interest (called \\"class\\" in the associated publications) with three possible values: 1) case, 2) control and 3) NA (neither case nor control). 1) Case: became persistently positive for at least two biochemical autoantibodies (GADA, IAA, IA2A or ZnT8A) and/or diagnosed with type 1 diabetes during the follow-up. 2) Control: remained autoantibody-negative throughout the follow-up. 3) NA: The remaining 51 individuals with a missing value (“NA”) did not qualify as cases or controls, since they were either persistently positive for only 1 biochemical autoantibody or transiently positive for one or more autoantibodies. We excluded these 51 individuals from the case-control-comparison but included them in the comparison between the sexes. Library preparation batch: The sequencing libraries were prepared in 7 batches. The names of the batches do not have any special meaning. That is, \\"1A\\" is not necessarily more similar to \\"1B\\" than it is to \\"3B\\". We treated this as a categorical technical variable with 7 categories. PC1 and PC2: Projections of the sample-specific methylation proportion vectors on the first two orthonormal principal components. The principal component analysis (PCA) was performed on the original coverage-filtered methylation proportion matrix (methylated/total reads), where missing values at each CpG site were imputed by the median over samples with non-missing values. The original methylation proportion matrix included 2752981 rows, whereas these publicly available matrices include 2548538 rows (all potential SNPs excluded). Hence, PCA on the publicly available data would result in slightly different values for PC1 and PC2. We included these as covariates in the differential methylation analysis to represent technical variation (in addition to the library preparation batches). References 1. Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, et al. Modernizing reference genome assemblies. PLoS Biol. 2011 Jul;9(7):e1001091. 2. Genome Reference Consortium. NCBI downloads: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz, accessed Feb 10th, 2019 3. NCBI. dbSNP: https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/common_all_20180423.vcf.gz, accessed April 29th, 2021 4. Gao S, Zou D, Mao L, Liu H, Song P, Chen Y, et al. BS-SNPer: SNP calling in bisulfite-seq data. Bioinformatics. 2015 Dec 15;31(24):4006–8.

Dataset Information

Small RNA mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation

Publications

Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation.

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