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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

Transient responding genes following serum stimulation. Bru-seq traces for NR4A3 (A), SAMD4 (B), KIRREL (C) and ABCA1 (D) during starved conditions and during different periods following serum addition. Data representation as in Fig. 2.
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BIO019323F3: Transient responding genes following serum stimulation. Bru-seq traces for NR4A3 (A), SAMD4 (B), KIRREL (C) and ABCA1 (D) during starved conditions and during different periods following serum addition. Data representation as in Fig. 2.

Mentions: While the previously described genes displayed sustained transcriptional induction or repression following serum stimulation, other genes demonstrated transient regulation. For example, the transcription factor gene NR4A3 was immediately induced after serum addition, but transcription returned to serum-starved levels within 60 min after stimulation (Fig. 3A). SAMD4A, encoding a RNA-binding protein, was also transiently induced and transcription returned to serum-starved levels after 60-90 min. As the SAMD4A gene is very long (>200 kb), there was a delay before the 3′ end of the gene experienced the effects of this brief pulse of transcriptional induction (Fig. 3B). We also observed genes such as KIRREL, encoding a signaling protein (Fig. 3C), and ABCA1, encoding a protein involved in cholesterol transport (Fig. 3D), that showed inhibition of productive initiation after serum addition followed by a reset to baseline expression.Fig. 3.


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)

Transient responding genes following serum stimulation. Bru-seq traces for NR4A3 (A), SAMD4 (B), KIRREL (C) and ABCA1 (D) during starved conditions and during different periods following serum addition. Data representation as in Fig. 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

BIO019323F3: Transient responding genes following serum stimulation. Bru-seq traces for NR4A3 (A), SAMD4 (B), KIRREL (C) and ABCA1 (D) during starved conditions and during different periods following serum addition. Data representation as in Fig. 2.
Mentions: While the previously described genes displayed sustained transcriptional induction or repression following serum stimulation, other genes demonstrated transient regulation. For example, the transcription factor gene NR4A3 was immediately induced after serum addition, but transcription returned to serum-starved levels within 60 min after stimulation (Fig. 3A). SAMD4A, encoding a RNA-binding protein, was also transiently induced and transcription returned to serum-starved levels after 60-90 min. As the SAMD4A gene is very long (>200 kb), there was a delay before the 3′ end of the gene experienced the effects of this brief pulse of transcriptional induction (Fig. 3B). We also observed genes such as KIRREL, encoding a signaling protein (Fig. 3C), and ABCA1, encoding a protein involved in cholesterol transport (Fig. 3D), that showed inhibition of productive initiation after serum addition followed by a reset to baseline expression.Fig. 3.

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