Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47152 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:DNA methylation and histone modifications encode epigenetic information. Recently, major progress was made to measure either mark at single-cell resolution. However, a method for simultaneous detection is lacking, preventing study of their interactions in complex systems. To bridge this gap, we developed scEpi2-seq. This technique provides single-molecule and single-cell readout of histone modifications and DNA methylation and reveals how DNA methylation maintenance is influenced by the local chromatin context.
2025-08-21 | GSE232637 | 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:Epigenetic modifications govern chromatin dynamics and cell state. However, current methods cannot simultaneously resolve the presence of multiple DNA modifications at co-occurring chromatin-associated features. It is thus not clear how these features are physically coupled and how their combinations regulate genome function. To address this key question, we report 6-base-CUT&Tag, a method for simultaneous 6-base sequencing at target chromatin features. Using 6-base-CUT&Tag to profile 5mC and 5hmC at co-occurring histone modifications in mouse embryonic stem cells, we identify histone mark-specific signatures of methylation and hydroxymethylation to improve discrimination of different functional enhancer states.
2026-01-15 | GSE296587 | GEO
Project description:DNA methylation and histone modifications are critical epigenetic regulators that orchestrate gene expression and modulate various physiological and pathological processes. However, existing methodologies for simultaneous profiling of these epigenetic marks often require high cell input and suffer from data loss due to bisulfite conversion. In this study, we present advanced multimodal chromatin profiling methods, MethylTag and Multi-MethylTag, that address these challenges by integrating Tn5 transposase with methylated adaptors and optimizing post-bisulfite library preparation. These methods enable high-resolution, multi-dimensional chromatin profiling with reduced cell input and improved data integrity. We validated these techniques in various human and mouse cell lines, revealing complex interactions between DNA methylation and histone modifications. Our findings highlight the utility of these approaches in enhancing epigenetic research and deepening our understanding of the regulatory mechanisms underlying gene expression.
2026-01-10 | GSE278068 | GEO
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: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: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