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Chromatin Immunoprecipitation (ChIP) to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
Published on: July 29, 2010
Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation
Ruijuan Li1, Weilong Guo, Jin Gu
1MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
Genomics
|July 25, 2012
Summary
External stimuli trigger dynamic gene expression changes. Fast-response genes show active chromatin, while slow-response genes have nucleosome occupancy. MicroRNAs regulate down-regulated genes, indicating multi-layer control.
Area of Science:
- Molecular Biology
- Genomics
- Cell Biology
Background:
- Gene expression is a dynamic process influenced by external stimuli.
- The precise factors governing gene expression changes post-stimulus remain incompletely understood.
Purpose of the Study:
- To investigate gene expression profiles in human umbilical vein endothelial cells (HUVEC) following Tumor Necrosis Factor (TNF) stimulation.
- To identify regulatory mechanisms distinguishing fast-response, slow-response, and down-regulated genes.
Main Methods:
- Analysis of gene expression profiles in HUVEC after TNF stimulus.
- Chromatin marker analysis (H3K27ac, H3K4me3) and Pol II/c-Myc binding assessment.
- Nucleosome occupancy studies in core-promoter regions.
- MicroRNA regulation analysis.
- Gene Ontology and promoter motif analysis.
Main Results:
- Fast-response up-regulated genes exhibit enrichment of active chromatin markers (H3K27ac, H3K4me3) and binding by Pol II and c-Myc.
- Slow-response up-regulated genes show frequent nucleosome occupancy in core-promoter regions.
- Down-regulated genes are significantly regulated by microRNAs.
- Gene clusters with distinct response behaviors display different functions and are governed by specific transcription factors.
Conclusions:
- Gene expression patterns upon external stimuli are regulated by a sophisticated interplay of multi-layer mechanisms.
- Chromatin state, transcription factor binding, nucleosome positioning, and microRNA activity collectively dictate cellular response dynamics.
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