dnase i hypersensitive site [dhs]  (Epigenomics ag)

Journal: Frontiers in Genetics

Article Title: Comparison of Capture Hi-C Analytical Pipelines

doi: 10.3389/fgene.2022.786501

Figure Lengend Snippet: Biologically relevant interactions. Bubble heat maps represent the proportion of interactions that overlap (A) . DHS or (B) . H3K4me1 peaks. The size of the circle represents the log10 number of promoter-other interactions identified by the different methods. (C) . A comparison between BCL2 promoter interactions in GM12878 cells within ± 1 Mb as reported by each method. Dashed lines represent examples of interactions that are identified in all tools (magenta), all tools except CHiCANE (blue), only in GOTHiC (yellow). ENCODE ChIP-seq profiles for DHS, H3K4me1 and H3K27ac in GM12878 cell lines are shown in the bottom tracks. DHS: DNase I Hypersensitivity sites.

Article Snippet: H3K27ac, H3K4me1 and H3K4me3 peaks and DNase I hypersensitivity sites (DHS; GM12878, H1) from the Roadmap Epigenomics Consortium (2015), heart DHS from the ENCODE project ( ) and Nuclease accessible sites (NAS; CD34 + ) from were downloaded using the AnnotationHub v2.22.1 R BioConductor package for GM12878 (record numbers “AH29709”, “AH29060”, “AH29061”, and “AH30743”, respectively) and CD34 + cells (record numbers “AH42424”, “AH42192”, “AH42194”, and “AH5085”, respectively), H1 cells (record numbers “AH29891”, “AH28878”, “AH28880”, and “AH29873”, respectively) and left ventricle/heart (record numbers “AH30592”, “AH29554”, “AH29555”, and “AH25530”, respectively).

Techniques: Comparison, ChIP-sequencing

Journal: Nature Communications

Article Title: 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells

doi: 10.1038/ncomms13426

Figure Lengend Snippet: ( a ) University of California Santa Cruz (UCSC) tracks showing chromosomal location and genes present in the 17q21 locus, containing a large haplotype block of asthma-associated SNPs; the location of asthma-risk SNP rs7216389 is indicated as blue line in the gene track. Black lines indicate SNPs' genomic location, and red lines are SNPs that overlap peaks of DNase hypersensitivity sites (DHS) from multiple cell types obtained from the ENCODE Encyclopedia (version 2) provided by the ENCODE Project Consortium (see Methods). Exemplary DHS tracks, H3K27ac and H3K4me1 enrichment tracks from CD4 + T cells, CD14 + monocytes and brain tissue (from ENCODE Project and NIH Epigenomics Roadmap Consortiums) are shown along with UCSC multispecies conservation tracks. ( b ) Distribution of asthma-associated 17q21 SNPs in different genomic regions. ( c ) The average number of DHS in the 17q21 locus of immune versus non-immune cell types ( n =10 and n =52, respectively) and ( d ) the 62 primary cell types (indicated as dots, profiled by the ENCODE Project Consortium, see Methods) ordered based on the number of DHS in the 17q21 locus. The top hits and discussed cell types are named and marked in red. ( e ) Overlap of DHS and 17q21 SNPs. ( f ) Number of DHS that directly overlap 17q21 SNPs in various cell types (full list in ). Error bars are mean±s.e.m.; *** P <0.001 by Student's unpaired two-tailed t -test, and following Bonferroni correction for multiple testing.

Article Snippet: Here we utilized the comprehensive DNase I hypersensitivity sites (DHS) data sets, generated by the ENCODE Project and NIH Epigenomics Roadmap Consortiums , to first define the cell types where the 17q21 locus is selectively more active, that is, harbour a significantly higher number of cis -regulatory elements (DHS), as these cell types are more likely to be affected by the ncSNPs present in the locus.

Techniques: Blocking Assay, Two Tailed Test