Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47152 | ENA |
REPOSITORIES: ENA
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Project description:It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic binding sites of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS showed similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further revealed that H3K4me1-marked regions are mostly CpG-poor, lack of methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenario with precious biological samples.
2021-10-20 | GSE179266 | GEO
Project description:We present Nanopore-DamID, a method to simultaneously detect cytosine methylation and DNA-protein interactions from single molecules, via selective sequencing of adenine-labelled DNA. Assaying LaminB1 and CTCF binding with Nanopore-DamID, we identify escape from LAD-associated repression of hypomethylated promoters amidst generalised hypermethylation of LaminB1-associated regulatory elements. We detect novel CTCF binding sites in highly repetitive regions, and allele-specific CTCF binding to imprinted genes and the active X chromosome. Nanopore-DamID highlights the importance of DNA methylation to transcription factor activity.
2025-05-15 | GSE203109 | GEO
Project description:In mammals, dosage compensation for the sex chromosomes is achieved by transcriptional silencing of one of the two X chromosomes in females. The inactive X adopts a particular epigenetic state, characterised by specific histones, histone marks, DNA methylation and 3D chromatin structure. As allelic resolution with short-read sequencing is limited, we do not yet have chromosome-wide phased methylomes of the active and inactive X. In this study, we obtained such complete X methylomes in mouse placenta and neural stem cells (NSCs) via long-read nanopore sequencing. This accession corresponds to the RNA-seq for the NSCs.
2024-10-31 | E-MTAB-14486 | biostudies-arrayexpress
Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).
2023-09-22 | E-MTAB-12247 | biostudies-arrayexpress
Project description:Chemical modification of histone proteins by methylation plays a central role in chromatin regulation by recruiting epigenetic ‘readers’ via specialized binding domains. Depending on the degree of methylation, the exact modified amino acid, and the associated reader proteins histone methylations are involved in the regulation of all DNA-based processes, such as transcription, DNA replication, and DNA repair. We have previously established a method that allows the unbiased identification of nuclear proteins which binding to nucleosomes is regulated by the presence of specific histone modifications (1,2). The method is based on an in-vitro reconstitution of semi-synthetic nucleosomes bearing a predefined set of histone modifications which are subsequently used as baits for affinity purification pull-down experiments with nuclear extracts followed by identification and quantification of nucleosome-interacting proteins using LC-MS/MS. Here we provide a representative set of label-free MS results for nucleosome pull-down affinity purification experiments performed using unmodified as well as H3K4me3- and H3K9me3-modified di-nucleosomes and nuclear extract obtained from HeLa S3 cells. 1. Bartke T, Vermeulen M, Xhemalce B, Robson SC, Mann M, Kouzarides T (2010) Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143:470-484 2. Makowski MM, Gräwe C, Foster BM, Nguyen NV, Bartke T, Vermeulen M (2018) Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry. Nat Commun 9:1653
2022-08-11 | PXD027238 | Pride
Project description:Here we describe the application of high-throughput sequencing technology for profiling histone and DNA methylation, and gene expression patterns of normal human mammary progenitor-enriched and luminal lineage-committed cells. We observed significant differences in histone H3 lysine 27 tri-methylation (H3K27me3) enrichment and DNA methylation of genes expressed in a cell type-specific manner, suggesting their regulation by epigenetic mechanisms and a dynamic interplay between the two processes that together define developmental potential. The technologies we developed and the epigenetically regulated genes we identified will accelerate the characterization of primary cell epigenomes and the dissection of human mammary epithelial lineage-commitment and luminal differentiation. Examination of histone H3K27me3 modifications in 2 cell types from 3 individuals and H3K4me3 modifications in 2 cell types from one individual sample.
2011-03-01 | E-GEOD-26137 | biostudies-arrayexpress
Project description:Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation. Paired-end bisulphite sequencing of H3K27me3-ChIP DNA for LNCaP and PrEC cell lines
2012-01-18 | E-GEOD-30558 | biostudies-arrayexpress
Project description:The newly discovered 5-hydroxymethylcytosine (5hmC) may complicate previous observations of abnormal cytosine methylation statuses used for the identification of new tumor suppressor gene candidates relevant to human hepatocarcinogenesis. The simultaneous detection of 5mC and 5hmC will stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma (HCC). Here, we performed a newly developed single-base high-throughput sequencing approach (hydroxymethylation and methylation Sensitive Tag sequencing, HMST-seq) to synchronously measure these two modifications in HCC samples. After identifying the differentially methylated and hydroxymethylated genes in HCC, we integrated the DNA copy-number alterations as determined using array-based comparative genomic hybridization (aCGH) data with gene expression to identify genes potentially silenced by promoter hypermethylation. As a result, we report a high enrichment of genes with epigenetic aberrations in cancer signaling pathways. Six genes were selected as tumor suppressor gene (TSG) candidates, among which, ECM1, ATF5 and EOMES were confirmed to have potential anti-cancer function via siRNA experiments. To fully examine 5mC and 5hmC status in HCC, we used a newly developed single-base high-throughput sequencing approach (hydroxymethylation and methylation sensitive tag sequencing, HMST-seq) to synchronously measure these two modifications in HCC samples and their adjacent non-cancerous liver tissues (non-HCCs).
2014-09-01 | E-GEOD-54141 | biostudies-arrayexpress
Project description:There are three major epigenetic mechanisms, DNA methylation, histone modifications, and ncRNAs. The histone is a key player in epigenetics, and the acetylation and methylation are their most common post-translational modifications (PTMs). These histone modifications have important roles in transcriptional regulation, DNA repair, DNA replication, alternative splicing and chromosome condensation. For example, we previously found that H3.3 lysine 36 trimethylation (H3.3K36me3) histone and its reader protein BS69 could work together to regulate pre-mRNA process. Therefore, in this study, we established in vitro histone acetylation, demethylation and methylation models, respectively, by using human lung, liver and colorectal cancer cells.
2022-03-02 | PXD002453 | Pride
Project description:Nanopore Sequencing and assembly of Col-0 carrying seed coat expressed GFP and RFP transgenes flanking the centromere of chromosome 3 (CTL 3.9) - additionally, DNA methylation was derived using deepsignal-plant using these reads.
2024-01-20 | E-MTAB-13686 | biostudies-arrayexpress