Enhancer (genetics) A short region of DNA that can increase transcription of genes Promoter An additive that increases the activity of a catalyst. Enhancer One who enhances; one who, or that which, raises the amount, price, etc. Promoter One that promotes, especially an active supporter or ad...
Density: number of enhancer-promoter plasmids. c. Fraction of remaining enhancer-promoter plasmids passing DNA (>25) and RNA (>1) threshold (y-axis) with downsampling of sequencing reads (x-axis). d. Distribution of plasmid barcodes per enhancer-promoter pair, red dotted-line is threshold ...
Here, we present PSYCHIC, a computational approach for analyzing Hi-C data and identifying promoter–enhancer interactions. We use a unified probabilistic model to segment the genome into domains, which we then merge hierarchically and fit using a local background model, allowing us to identify ...
Lastly, to test whether chromatin state at enhancers alters gene expression, we measured gene expression at both genes nearest to each enhancer (data not shown), as well as a subset of promoters with previously confirmed Hi-C interactions with DNA methylation-sensitive enhancers we identified (Shen...
Coronary artery disease (CAD) is a multifactorial disorder, which is partly heritable. Herein, we implemented a mapping of CAD-associated candidate genes by using genome-wide enhancer-promoter conformation (H3K27ac-HiChIP) and expression quantitative tra
如果仅仅只是分析部分染色质片段之间的互作,最经典的莫过于研究promoter与其他染色质片段的互作,比如研究enhancer-promoter的互作,此时利用全基因组的Hi-C文库代价太大,而传统的3C,4C又无法满足要求。基于这样的一个需求驱动,Promoter Capture Hi-C技术应用而生。
Chalfun A, Mes JJ, Mlynarova L, Aarts MGM, Angenent GC (2003) Low frequency of T-DNA based activation tagging in Arabidopsis is correlated with methylation of CaMV 35S enhancer sequences. FEBS Lett 555:459–463 ArticleCASGoogle Scholar ...
One such composite promoter, CAG, consists of theCMVenhancer fused to the promoter and first intron of chicken (or human skeletal) β-actin. Its activity is equivalent to, or in some cell types exceeds that of CMV[14–21]. Because of this robust activity, theCAG promoteris quite popular ...
Nevertheless, it remains debatable whether TAD boundaries can absolutely prevent an enhancer from interacting with and activating a gene in another TAD30,31,32,33,34. Our genome-wide analysis uncovered that, although loop interactions largely decay across distance (Extended Data Fig. 1j), ~22.5% ...
Bar plot shows the fraction of enhancers that are significantly downregulated (IBDdown, gray) or upregulated (IBDup, white) in UCa and CDa vs. Ctrl, grouped by the number of enhancers within an enhancer cluster. Enhancers not part of clusters are included for comparisons (singleton enhancers)...