Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Authors | |
Abstract | 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-κB 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. |
Year of Publication | 2016
|
Journal | Cell Syst
|
Volume | 2
|
Issue | 5
|
Pages | 323-34
|
Date Published | 2016 May 25
|
ISSN | 2405-4712
|
URL | |
DOI | 10.1016/j.cels.2016.04.011
|
PubMed ID | 27211859
|
PubMed Central ID | PMC5032147
|
Links | |
Grant list | P30 DK043351 / DK / NIDDK NIH HHS / United States
R01 DK097485 / DK / NIDDK NIH HHS / United States
U19 AI109725 / AI / NIAID NIH HHS / United States
|