Project description:Super-enhancer (SE) plays a vital role in the determination of cell identity and cell fate through the control of cell- or tissue-specific gene regulation. Upregulated expression of coding genes is frequently associated with SE. However, the transcription dysregulation driven by SE, from long non-coding RNAs (lncRNAs) viewpoint, remains unclear. Here, SE-associated lncRNAs in HCC were comprehensively screened.
Project description:Super-enhancer (SE) plays a vital role in the determination of cell identity and cell fate through the control of cell- or tissue-specific gene regulation. Upregulated expression of coding genes is frequently associated with SE. However, the transcription dysregulation driven by SE, from long non-coding RNAs (lncRNAs) viewpoint, remains unclear. Here, SE-associated lncRNAs in HCC were comprehensively screened. The result shows that pol2-mediated transcription of SE-associated lncRNAs is more sensitive to JQ1 treatment in a genome-wide manner.
Project description:Here we apply integrated epigenomic and transcriptomic profiling to uncover super-enhancer heterogeneity between breast cancer subtypes, and provide clinically relevant biological insights towards TNBC. Using CRISPR/Cas9-mediated gene editing, we identify genes that are specifically regulated by TNBC-specific super-enhancers, including FOXC1 and MET, thereby unveiling a mechanism for specific overexpression of the key oncogenes in TNBC. We also identify ANLN as a novel TNBC-specific gene regulated by super-enhancer. Our studies reveal a TNBC-specific epigenomic landscape, contributing to the dysregulated oncogene expression in breast tumorigenesis.
Project description:Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. lncRNAs (long non-coding RNAs) play a significant role in the occurrence and development of PCa. eRNAs (enhancer RNA) and SE-lncRNAs (super-enhancer lncRNA) are important elements of lncRNAs, but the role of eRNAs and SE-lncRNAs in PCa remains largely unclear. In this work, we identified 681 eRNAs and 292 SE-lncRNAs that were expressed differentially in PCa using a microarray. We constructed a transcriptional regulation network that eRNA related enhancer and the target genes shared the same TF binding motifs. Further, we investigated whether CTCF played a role in mediating the transcriptional regulation network. eRNAs, especially those that regulate androgen response genes, may be candidates for prognostic biomarkers and therapy targets. Our work provide a new perspective for developing medical treatments and therapies for prostate cancer.
Project description:Purpose: Examine H3K27ac enhancer and super-enhancer landscape differences between primary colorectal carcinoma and adjacent normal mucosa towards the identification of novel downstream targets. Methods: H3K27ac ChIP-seq and RNA-seq were performed on fresh primary colorectal carcinoma samples and normal colonic mucosa, from human patient samples. Results: We identified 2026 total super-enhancers in our cohort, between primary colorectal and normal mucosa. We quantified differences in H3K27ac signal within this space, between tumor and normal, and identified putative downstream target genes through integration with sample matched RNA-seq using a positive linear correlation model to identifty putative target genes.