Project description:The lncRNA EPR (a.k.a BC030870) is highly enriched in the gastrointestinal tract in mice and, more specifically, in the large intestine. We generated conditional EPR knock-out in large intestine e and analyzed genome-wide the gene expression changes by RNA-Seq. Total RNA was extracted from the proximal colon of six control (EPR fl/fl) and six knock-out (EPR cKO) mice. Libraries were constructed and sequenced. Results indicate that EPR knock-out predominantly leads to down-regulation of genes implicated in mucus biogenesis. These results help in explaining the phenotype displayed by EPR cKO mice that is characterized by higher susceptibility to intestinal inflammation and cancer formation.
Project description:The lncRNA EPR (a.k.a BC030870) is highly enriched in the gastrointestinal tract in mice and, more specifically, in the large intestine. We generated conditional EPR knock-out in large intestine e and analyzed genome-wide the gene expression changes by RNA-Seq. Total RNA was extracted from the proximal colon of six control (EPR fl/fl) and six knock-out (EPR cKO) mice. Libraries were constructed and sequenced. Results indicate that EPR knock-out predominantly leads to down-regulation of genes implicated in mucus biogenesis. These results help in explaining the phenotype displayed by EPR cKO mice that is characterized by higher susceptibility to intestinal inflammation and cancer formation.
Project description:EPR, a lncRNA present in the chromatin fraction of NMuMG cells, controls proliferation and fate determination in mammary gland cells. We wanted to define if EPR overexpression in NMuMG cells affects the landcape of two histone activation marks (H3K4me3 and H3K27ac).
Project description:We have previously shown that EPR favors the interaction between Mettl7a1 promoter and a distal enhancer element. To comprehensively map long-range interactions between promoters and distal regulatory elements that are affected by EPR KO in large intestine, we preformed Promoter capture Hi-C experiments. Crypts were purified from proximal colon of two EPR fl/fl control and two EPR cKO mice. Hi-C libraries were constructed and hybridized with biotinylated RNA probes from the Arima mouse promoter panel designed to hybridize the promoters of 25752 mouse genes. Captured libraries were sequenced and bioinformatically analyzed. Our results indicate that EPR knockout leads to a rewiring of a number of promoter-enhancer interactions.