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Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing
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DOI：10.1016/j.cels.2016.04.011.png)
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Abstract
En 中文
Reporter gene assays are a venerable tool for studying signaling pathways, but they lack the throughput and complexity necessary to contribute to a systems-level understanding of endogenous signaling networks. We present a parallel reporter assay, transcription factor activity sequencing (TF-seq), built on synthetic DNA enhancer elements, which enables parallel measurements in primary cells of the transcriptome and transcription factor activity from more than 40 signaling pathways. Using TF-seq in Myd88 (-/-) macrophages, we captured dynamic pathway activity changes underpinning the global transcriptional changes of the innate immune response. We also applied TF-seq to investigate small molecule mechanisms of action and find a role for NF-B-k activation and coordination of the STAT1 response in the macrophage reaction to the anti-inflammatory natural product halofuginone. Simultaneous TF-seq and global gene expression profiling represent an integrative approach for gaining mechanistic insight into pathway activity and transcriptional changes that result from genetic and small molecule perturbations.
Keywords:
ENRICHMENT ANALYSIS
CHIP-SEQ
TRANSCRIPTION
REGULATORS
CHROMATIN
HALOFUGINONE
DISSECTION
MOLECULES
ENHANCERS
KNOWLEDGE
Journal
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7.7
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1.4K
Citations:
1.0W
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