There are plenty of reports dealing with serum-dependent/stimulated gene expression profiling in mammalian cells (for example: http://www.ncbi.nlm.nih.gov/pubmed/9872747). These studies usually take serum-deprived cells and add back serum. Over several time points, the total RNA is isolated and profiled. What results is the characterization of a transcription profile inducible by serum. However, I have not found a comparison of normal, pre-starvation transcription profile with that of a serum-starved condition. Does anyone know of any such report? It is assumed that serum starvation induces a G0/G1-like state of quiescence (this view is contested by Cooper's publications; see http://www.ncbi.nlm.nih.gov/pubmed/9666815 and later ones), and it is assumed that this supposed "cell-cycle quiescence" also reflects a state of "transcriptional quiescence". Is it true? Does anyone know of any reports that definitively implicates serum-starvation in acquisition of transcriptional quiescence? What is the transcriptome of a serum-starved cell like? Any input/insight/suggestion will be appreciated. A request: please do not include whole-organism starvation models--if you find any--in your answer, as they do not reflect cultured cell profiles accurately.
Hi Anil,
Thank you for an interesting question. It does not appear that serum starvation leads to “transcription quiescence”. Here is the report on “growth arrest specific” (gas) genes from 1988 (the genes up-regulated in starved cells were identified by subtraction of cDNA library from NIH 3T3 grown in 20% serum from the library obtained from the cells cultured in 0.5% serum): http://www.ncbi.nlm.nih.gov/pubmed/3409319. The “gas” genes turned out to be important in development and one (gas-6) participates in blood clotting.
The following (more recent) papers describe changes in expression of individual genes or group of genes induced by serum deprivation:
Time course of lysosomal membrane protein DRAM induction upon serum withdrawal from liver cancer cells: http://www.ncbi.nlm.nih.gov/pubmed/23251372
Genes induced and repressed in primary murine cortical cells during programmed cell death caused by serum deprivation: http://www.jbmb.or.kr/fulltext/jbmb/view.php?vol=40&page=277
Changes in lipid metabolism of retrovirus packaging cells in the absence of serum or in reduced serum: http://www.ncbi.nlm.nih.gov/pubmed/22179842
Changes in transcript profile in primary human endothelial cells: http://www.ncbi.nlm.nih.gov/pubmed/20360594
Characterization of transcriptome multilineage differentiating stress-enduring cell population (stress means serum deprivation, collagenase treatment, and hypoxia):
http://www.ncbi.nlm.nih.gov/pubmed/23755141
Genes down-regulated during G1 arrest induction by serum starvation:
http://www.ncbi.nlm.nih.gov/pubmed/18202766
Hope this helps,
Maria
Hi Anil,
Thank you for an interesting question. It does not appear that serum starvation leads to “transcription quiescence”. Here is the report on “growth arrest specific” (gas) genes from 1988 (the genes up-regulated in starved cells were identified by subtraction of cDNA library from NIH 3T3 grown in 20% serum from the library obtained from the cells cultured in 0.5% serum): http://www.ncbi.nlm.nih.gov/pubmed/3409319. The “gas” genes turned out to be important in development and one (gas-6) participates in blood clotting.
The following (more recent) papers describe changes in expression of individual genes or group of genes induced by serum deprivation:
Time course of lysosomal membrane protein DRAM induction upon serum withdrawal from liver cancer cells: http://www.ncbi.nlm.nih.gov/pubmed/23251372
Genes induced and repressed in primary murine cortical cells during programmed cell death caused by serum deprivation: http://www.jbmb.or.kr/fulltext/jbmb/view.php?vol=40&page=277
Changes in lipid metabolism of retrovirus packaging cells in the absence of serum or in reduced serum: http://www.ncbi.nlm.nih.gov/pubmed/22179842
Changes in transcript profile in primary human endothelial cells: http://www.ncbi.nlm.nih.gov/pubmed/20360594
Characterization of transcriptome multilineage differentiating stress-enduring cell population (stress means serum deprivation, collagenase treatment, and hypoxia):
http://www.ncbi.nlm.nih.gov/pubmed/23755141
Genes down-regulated during G1 arrest induction by serum starvation:
http://www.ncbi.nlm.nih.gov/pubmed/18202766
Hope this helps,
Maria
Hi Maria,
Thank you very much for such a detailed response with links. These reports and many others that I screened reveal that serum-deprivation causes suppression of some genes while activation of some others. But it is still not clear to me whether global transcription slows down upon serum-deprivation. I still do not get the whole picture here: like, how many genes go down by what fold, and how many go up by what fold. I am suspecting--based on secondary inferences from some of my recent experiments, which I am unable to detail at the moment--that global on-going transcription (but not necessarily the global transcript level, which might stay a bit stable for a little while depending on life span of individual transcripts). I might do a quick RNA pulse-labeling experiment.
By the way, I think you are the one who looked (and still looking) into the mechanistic conflicts between the Pol II and nucleosomes. I shall never forget the thrill of reading those pioneering papers from Gary's lab in early 1990s, and this field still fascinates me--including your papers (both from 2002, 2005, 2008).
Best wishes,
Anil
Dr. Hilary Coller of Princeton Univ. kindly suggested me this article in this regard:
http://www.ncbi.nlm.nih.gov/pubmed/993273.
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