dnase i hypersensitive sites sequencing  (Epigenomics ag)

Journal: BMC Genomics

Article Title: Genome-wide enhancer-gene regulatory maps of liver reveal novel regulatory mechanisms underlying NAFLD pathogenesis

doi: 10.1186/s12864-025-11668-w

Figure Lengend Snippet: Study overview. Left: Construction of the ABC enhancer-gene maps of liver. The epigenomic data, including ATAC-seq, DNase-seq, H3K27ac ChIP-seq and HiC-seq data were from 15 liver biosamples. The bar chart represents the characteristics of ABC maps. Middle: We integrated the constructed ABC regulatory maps of liver and the NAFLD GWASs. Manhattan plots show the genome-wide association statistics of the discovery and replication cohorts, and the validated ABC SNPs. Right: The characterization of ABC SNPs and target genes, with the graphic summary of connecting rs2017869 within the non-coding region to NAFLD pathogenesis. Heatmaps show the characterization of ABC SNPs. Bar chart of pathway enrichment analyses and drug-gene interaction network represent the characterization of ABC genes. ABC, Activity-by-Contact; ATAC-seq, assay for transposase-accessible chromatin using sequencing; DNase-seq, DNase I hypersensitive sites sequencing; H3K27ac ChIP-seq, H3K27ac chromatin immunoprecipitation sequencing; Hi-C, high-throughput chromosome conformation capture; NAFLD, non-alcoholic fatty liver disease; GWAS, genome-wide association study; SNP, single nucleotide polymorphism; GGT1 , gamma-glutamyltransferase 1

Article Snippet: To construct Activity-by-Contact (ABC) maps for liver tissues and cell lines, we curated published epigenomic data, including DNase I hypersensitive sites sequencing (DNase-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), H3K27ac chromatin immunoprecipitation sequencing (H3K27ac ChIP-seq) and high-throughput chromosome conformation capture (Hi-C) data from ENCODE [ ] and the Roadmap Epigenomics Project [ ].

Techniques: ChIP-sequencing, Construct, GWAS, Activity Assay, Sequencing, Hi-C, High Throughput Screening Assay

Journal: Blood

Article Title: 13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking

doi: 10.1182/blood.2019004684

Figure Lengend Snippet: Genetic mapping and epigenetic landscape of the 13q12.2 locus. Map of the FLT3 and PAN3 loci in 13q12.2. Predicted topologically associating domains based on data from the lymphoblastic GM12878 cell line are indicated by diagonal dashed lines. (A) Hemizygous deletions identified in 27 BCP ALL samples by WGS (black) or SNP array or WES (gray). The violet square corresponds to the minimally deleted region. (B) DNase-seq signal based on the GM12878 cell line. (C) ATAC-seq signal based on the NALM-6 cell line. (D) ChIP-seq of histone modifications (H3K27ac and H3K4me3) based on the GM12878 (E) and the NALM-6 cell lines. (F) H3K27ac- and H3K4me3-enriched PLAC-seq interaction map based on the NALM-6 cell line. (G) Relative interaction frequencies in 13q12.2 in 6 primary ALL cases and the GM12878 cell line based on Hi-C, where higher values on the y-axis correspond to stronger interaction. Increased interactions with the enhancer element DS3 are seen in the case with 13q12.2 deletion.

Article Snippet: Chromatin structure and ChIP-seq data mining GM12878 histone marks chromatin immunoprecipitation (ChIP)-sequencing (ChIP-seq) data (H3K27ac and H3K4me3) and DNase I–hypersensitive site sequencing (DNase-seq) data (bigwig files) were downloaded from the University of California, Santa Cruz (UCSC) database ( http://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixHuman.html ).

Techniques: ChIP-sequencing, Hi-C

Journal: Frontiers in Genetics

Article Title: The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment

doi: 10.3389/fgene.2019.00754

Figure Lengend Snippet: Genotype-dependent suppression and tissue specificity of CTSW expression. (A) The violin plot of CTSW expression levels in three genotype groups at rs3903072, using the TCGA ER+ breast cancer patient data. The p -value is for the coefficient of genotype in multivariate linear regression with adjustment for gene copy number. (B) Survival analysis of breast cancer patients based on CTSW expression levels. The p -value is from the log-rank test using the two groups separated by the median expression of CTSW . (C) The CTSW promoter chromatin accessibility in multiple cell lines from various tissue origins. The top ENCODE plot shows the DNase I hypersensitivity (DHS) uniform peaks in ENCODE tier 1 cell lines, along with the tier 2/3 cells in which CTSW promoter is open. The bottom plot shows the DHS signals for primary cells from Roadmap Epigenomics data. Cells with breast tissue origin are marked as cyan, and blood-related normal or cancer cells are marked as magenta. HMPC, hematopoietic multipotent progenitor cells; CMP CD34+, common myeloid progenitor cells CD34+. (D) Distribution of CTSW expression in cell lines and in tissues. The top figure shows data from BioGPS, displaying only 10 cell types with highest CTSW expression. The bottom figure shows data from GTEx, displaying only nine tissue types with highest CTSW expression and mammary tissue (ranked 13th).

Article Snippet: Second, the CTSW promoter region is not accessible in normal mammary cells or breast cancer cells (HMEC, MCF-7, T-47D) but is open in CD8+ T cells, CD56+ NK cells, CD34+ common myeloid progenitor cells, and the acute T cell leukemia cell line Jurkat , according to the DNase I hypersensitive sites sequencing (DNase-seq) data from ENCODE and the Roadmap Epigenomics Project.

Techniques: Expressing