Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

@article{Giannakakis2015ContrastingEP,
  title={Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress},
  author={Antonis Giannakakis and Jingxian Zhang and Piroon Jenjaroenpun and Srikanth Nama and Norliyana Zainolabidin and Meiyee Aau and Aliaksandr A. Yarmishyn and Candida Vaz and Anna V. Ivshina and Oleg V Grinchuk and Mathijs Voorhoeve and Leah A. Vardy and Prabha Sampath and Vladimir A. Kuznetsov and Igor Kurochkin and Ernesto Guccione},
  journal={Scientific Reports},
  year={2015},
  volume={5}
}
Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription characterized by pausing of RNA polymerase II (PolII) in both directions, at specific promoters, within 30 minutes of the OS response. In contrast to protein-coding genes, which are commonly down… 
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References

SHOWING 1-10 OF 86 REFERENCES
A global non-coding RNA system modulates fission yeast protein levels in response to stress
TLDR
An extensive array of ncRNAs with trans associations that have the potential to influence multiple pathways are described, including non-coding transcripts that regulate specific stress responses, adding unanticipated information-processing capacity to the MAPK signalling system.
Transcription of Satellite III non-coding RNAs is a general stress response in human cells
TLDR
This work uses real-time RT-PCR to study the expression of repetitive Satellite III DNA in pericentromeric heterochromatin and finds that C-rich transcripts are almost undetectable in unstressed cells and modestly increase after stress, while G-rich RNAs are induced by a wide range of stress treatments.
Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence
TLDR
It is proposed that the senescence-associated changes in TTR-RBPs directly contribute to the impaired responses to oxidant damage that characterize cellularsenescence and advancing age.
The Non-coding RNA gadd7 Is a Regulator of Lipid-induced Oxidative and Endoplasmic Reticulum Stress*
TLDR
Together these data are the first to implicate a non-coding RNA in a feed-forward loop with oxidative stress and its induction of the endoplasmic reticulum stress response.
HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts
TLDR
It is shown for the first time a functional link between oxygen deprivation and the modulation of long noncoding transcripts from ultraconserved regions, termed transcribed-ultraconserved regions (T-UCRs), and that the hypoxia-inducible factor (HIF) is at least partly responsible for the induction of several members of this group.
Whole genome analysis of p38 SAPK-mediated gene expression upon stress
TLDR
Genome-wide transcriptional analyses on mouse embryonic fibroblasts treated with three different p38 SAPK activating-stimuli shows a selective response to specific stimuli and a restricted common response of up to 20% of the stress up-regulated early genes that involves an important set of transcription factors that might be critical for either cell adaptation or preparation for continuous extra-cellular changes.
Identification and Characterization of Novel Genotoxic Stress-Inducible Nuclear Long Noncoding RNAs in Mammalian Cells
TLDR
The results suggest that distinct sets of nuclear long ncRNAs play roles in cellular defense mechanisms against specific genotoxic agents, and that particular long nCRNAs have the potential to be surrogate indicators of a specific cell stress.
...
...