ArticleNucleic acids research2012
Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
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- A β-Catenin-TCF-Sensitive Locus Control Region Mediates GUCY2C Ligand Loss in Colorectal Cancer.Cellular and molecular gastroenterology and hepatology · 2022Article
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- APC-β-catenin-TCF signaling silences the intestinal guanylin-GUCY2C tumor suppressor axis.Cancer biology & therapy · 2020Article
- Identification of β-catenin target genes in colorectal cancer by interrogating gene fitness screening data.Oncology letters · 2019Article
- Facilitating Analysis of Publicly Available ChIP-Seq Data for Integrative Studies.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2019Article
- Unraveling the role of peroxisome proliferator-activated receptor-β/δ (PPARβ/δ) expression in colon carcinogenesis.NPJ precision oncology · 2019Review
- PRSS8 suppresses colorectal carcinogenesis and metastasis.Oncogene · 2019Article
- CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands.Epigenetics & chromatin · 2018Article
- CRISPR-Mediated Reorganization of Chromatin Loop Structure.Journal of visualized experiments : JoVE · 2018Article
- Multiproteomic and Transcriptomic Analysis of Oncogenic β-Catenin Molecular Networks.Journal of proteome research · 2018Article
- Epigenetic regulation of transcriptional plasticity associated with developmental song learning.Proceedings. Biological sciences · 2018Article
- Chromatin Conformation Links Distal Target Genes to CKD Loci.Journal of the American Society of Nephrology : JASN · 2018Article
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7 authors.
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Abstract
Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RNA polymerase II (Pol II), but are also affected by RNA turnover rate. Here, we demonstrate that integrated analysis of genome-wide TF occupancy, Pol II binding and steady-state RNA levels provide important insights in gene regulatory mechanisms. Pol II occupancy, as detected by Pol II ChIP-seq, was found to correlate better with TF occupancy compared to steady-state RNA levels and is thus a more precise readout for the primary transcriptional mechanisms that are triggered by signal transduction. Furthermore, analysis of differential Pol II occupancy and RNA-seq levels identified genes with high Pol II occupancy and relatively low RNA levels and vice versa. These categories are strongly enriched for genes from different functional classes. Our results demonstrate a complementary value in Pol II chip-seq and RNA-seq approaches for better understanding of gene expression regulation.
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