Project description:Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Mosaic-Seq of beta-globin locus (pooled infection)
Project description:Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Mosaic-Seq of beta-globin locus (separate infection)
Project description:Single-cell perturbation assays such as Mosaic-seq enable highly multiplexed functional assessment of enhancers in their endogenous genomic context. By introducing a few computational and experimental improvements, we expanded the Mosaic-seq analysis to capture the secondary gene targets of enhancers. Our analysis of >500 putative enhancers in K562 cells demonstrates that many secondary hits are shared among enhancers targeting different transcriptional factors, which reveals an interwoven enhancer-driven gene regulatory network. Together, our data underscore the flexibility of manipulating gene transcription by modifying enhancer activity.
Project description:Single-cell perturbation assays such as Mosaic-seq enable highly multiplexed functional assessment of enhancers in their endogenous genomic context. By introducing a few computational and experimental improvements, we expanded the Mosaic-seq analysis to capture the secondary gene targets of enhancers. Our analysis of >500 putative enhancers in K562 cells demonstrates that many secondary hits are shared among enhancers targeting different transcriptional factors, which reveals an interwoven enhancer-driven gene regulatory network. Together, our data underscore the flexibility of manipulating gene transcription by modifying enhancer activity.
Project description:Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Human/mouse mixing Drop-Seq experiments for K562 and MEFs
Project description:Unraveling the complexity of transcriptional programs coded by different cell types has been one of the central goals of cell biology. Using genome-wide location analysis, we examined how two different cell types generate different responses to the NF-kappaB signaling pathway. We showed that, after tumor necrosis factor-alpha (TNF-alpha) treatment, NF-kappaB p65 subunit binds to distinct genome locations and subsequently induces different subsets of genes in human monocytic THP-1 cells versus HeLa cells . Interestingly, the differential p65 binding in two cell types correlates with pre-existing cell-type specific enhancers prior to TNF-alpha stimulation, marked by histone modifications. We also found that two transcription factors, PU.1 and C/EBPalpha, appear to synergistically mediate enhancer creation and affect NF-kappaB target selection in THP-1 cells. In HeLa cells, co-expression of PU.1 and C/EBPalpha conferred TNF-alpha responsiveness to a subset of THP-1 specific NF-kappaB target genes. These results suggest that the diversity of transcriptional programs in mammalian cells arises, at least in part, from pre-existing enhancers that are established by cell specific transcription factors. We used Affymetrix microarray (GPL570) to obtain gene expression data for THP1 and HeLa cells before and after TNF-alpha treatment.
