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Capturing the dynamic nascent transcriptome during acute cellular responses: The serum response.

Kirkconnell KS, Paulsen MT, Magnuson B, Bedi K, Ljungman M - Biol Open (2016)

Bottom Line: Surprisingly, transcription of important DNA damage response genes and histone genes were rapidly repressed.We also show that RNA polymerase II accelerates as it transcribes large genes and this was independent of whether the gene was induced or not.These results provide a unique genome-wide depiction of dynamic patterns of transcription of serum response genes and demonstrate the utility of Bru-seq to comprehensively capture rapid and dynamic changes of the nascent transcriptome.

View Article: PubMed Central - PubMed

Affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

No MeSH data available.


Related in: MedlinePlus

Gene set enrichment analysis of serum response genes. Enriched pathways identified by DAVID in induced (A) and inhibited (B) gene sets during each serum-stimulated labeling period. The −log10 values of P-values are displayed. Enriched pathways identified by GSEA in induced (C), inhibited (D), and induced then inhibited (E) gene sets during each time point. Normalized enrichment scores (NES) are displayed.
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BIO019323F6: Gene set enrichment analysis of serum response genes. Enriched pathways identified by DAVID in induced (A) and inhibited (B) gene sets during each serum-stimulated labeling period. The −log10 values of P-values are displayed. Enriched pathways identified by GSEA in induced (C), inhibited (D), and induced then inhibited (E) gene sets during each time point. Normalized enrichment scores (NES) are displayed.

Mentions: We utilized the database for annotation, visualization and integrated discovery (DAVID) functional annotation tool to explore whether the serum response genes identified by Bru-seq were enriched for certain functional pathways, including known pathways related to serum activation. First we focused on the group of transcriptionally induced genes to identify potential pathways induced in response to serum stimulation. We found significant enrichment of genes related to cellular structures such as ‘focal adhesion’, ‘tight junctions’, ‘actin cytoskeleton’, and ‘extracellular matrix’ (Fig. 6A; Fig. S2), which are structures known to be important during the serum response and wound healing (Cooper et al., 2004; Iyer et al., 1999). Genes involved in various signaling pathways such as MAPK, chemokine, toll-like receptor, and TGF-β signaling were also enriched following serum stimulation. Enrichment of these pathways was seen during each labeling period.Fig. 6.


Capturing the dynamic nascent transcriptome during acute cellular responses: The serum response.

Kirkconnell KS, Paulsen MT, Magnuson B, Bedi K, Ljungman M - Biol Open (2016)

Gene set enrichment analysis of serum response genes. Enriched pathways identified by DAVID in induced (A) and inhibited (B) gene sets during each serum-stimulated labeling period. The −log10 values of P-values are displayed. Enriched pathways identified by GSEA in induced (C), inhibited (D), and induced then inhibited (E) gene sets during each time point. Normalized enrichment scores (NES) are displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920201&req=5

BIO019323F6: Gene set enrichment analysis of serum response genes. Enriched pathways identified by DAVID in induced (A) and inhibited (B) gene sets during each serum-stimulated labeling period. The −log10 values of P-values are displayed. Enriched pathways identified by GSEA in induced (C), inhibited (D), and induced then inhibited (E) gene sets during each time point. Normalized enrichment scores (NES) are displayed.
Mentions: We utilized the database for annotation, visualization and integrated discovery (DAVID) functional annotation tool to explore whether the serum response genes identified by Bru-seq were enriched for certain functional pathways, including known pathways related to serum activation. First we focused on the group of transcriptionally induced genes to identify potential pathways induced in response to serum stimulation. We found significant enrichment of genes related to cellular structures such as ‘focal adhesion’, ‘tight junctions’, ‘actin cytoskeleton’, and ‘extracellular matrix’ (Fig. 6A; Fig. S2), which are structures known to be important during the serum response and wound healing (Cooper et al., 2004; Iyer et al., 1999). Genes involved in various signaling pathways such as MAPK, chemokine, toll-like receptor, and TGF-β signaling were also enriched following serum stimulation. Enrichment of these pathways was seen during each labeling period.Fig. 6.

Bottom Line: Surprisingly, transcription of important DNA damage response genes and histone genes were rapidly repressed.We also show that RNA polymerase II accelerates as it transcribes large genes and this was independent of whether the gene was induced or not.These results provide a unique genome-wide depiction of dynamic patterns of transcription of serum response genes and demonstrate the utility of Bru-seq to comprehensively capture rapid and dynamic changes of the nascent transcriptome.

View Article: PubMed Central - PubMed

Affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

No MeSH data available.


Related in: MedlinePlus