scholarly journals Genome-wide polycomb target gene prediction in Drosophila melanogaster

2012 ◽  
Vol 40 (13) ◽  
pp. 5848-5863 ◽  
Author(s):  
Jia Zeng ◽  
Brian D. Kirk ◽  
Yufeng Gou ◽  
Qinghua Wang ◽  
Jianpeng Ma
Keyword(s):  
Drosophila Melanogaster ◽  
Target Gene ◽  
Gene Prediction ◽  
Genome Wide ◽  
Polycomb Target Gene

scholarly journals Regulatory Mechanisms of Metamorphic Neuronal Remodeling Revealed Through a Genome-Wide Modifier Screen in Drosophila melanogaster

Genetics ◽  
2017 ◽  
Vol 206 (3) ◽  
pp. 1429-1443 ◽  
Author(s):  
Dahong Chen ◽  
Tingting Gu ◽  
Tom N. Pham ◽  
Montgomery J. Zachary ◽  
Randall S. Hewes
Keyword(s):  
Drosophila Melanogaster ◽  
Regulatory Mechanisms ◽  
Neuronal Remodeling ◽  
Genome Wide ◽  
A Genome

scholarly journals Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Chong Wang ◽  
Luyao Zhang ◽  
Liangru Ke ◽  
Weiyue Ding ◽  
Sizun Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Growth ◽  
Cell Line ◽  
Poor Prognosis ◽  
Target Gene ◽  
Primary Effusion Lymphoma ◽  
Knock Out ◽  
Growth And Survival ◽  
Super Enhancer ◽  
Genome Wide

AbstractPrimary effusion lymphoma (PEL) has a very poor prognosis. To evaluate the contributions of enhancers/promoters interactions to PEL cell growth and survival, here we produce H3K27ac HiChIP datasets in PEL cells. This allows us to generate the PEL enhancer connectome, which links enhancers and promoters in PEL genome-wide. We identify more than 8000 genomic interactions in each PEL cell line. By incorporating HiChIP data with H3K27ac ChIP-seq data, we identify interactions between enhancers/enhancers, enhancers/promoters, and promoters/promoters. HiChIP further links PEL super-enhancers to PEL dependency factors MYC, IRF4, MCL1, CCND2, MDM2, and CFLAR. CRISPR knock out of MEF2C and IRF4 significantly reduces MYC and IRF4 super-enhancer H3K27ac signal. Knock out also reduces MYC and IRF4 expression. CRISPRi perturbation of these super-enhancers by tethering transcription repressors to enhancers significantly reduces target gene expression and reduces PEL cell growth. These data provide insights into PEL molecular pathogenesis.

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