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Title: Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress
Authors: Giannakakis, A
Zhang, J
Jenjaroenpun, P
Nama, S
Zainolabidin, N
Aau, M.Y
Yarmishyn, A.A
Vaz, C
Ivshina, A.V
Grinchuk, O.V 
Voorhoeve, M 
Vardy, L.A
Sampath, P 
Kuznetsov, V.A
Kurochkin, I.V
Guccione, E 
Keywords: complementary RNA
DNA directed RNA polymerase III
long untranslated RNA
messenger RNA
RNA polymerase II
transcription factor
untranslated RNA
binding site
cell line
chromatin immunoprecipitation
gene expression profiling
gene expression regulation
high throughput sequencing
human genome
oxidative stress
promoter region
protein synthesis
Binding Sites
Cell Line
Chromatin Immunoprecipitation
Computational Biology
Gene Expression Profiling
Gene Expression Regulation
Genome, Human
High-Throughput Nucleotide Sequencing
Oxidative Stress
Promoter Regions, Genetic
Protein Biosynthesis
RNA Polymerase II
RNA Polymerase III
RNA, Antisense
RNA, Long Noncoding
RNA, Messenger
RNA, Untranslated
Transcription Factors
Issue Date: 2015
Citation: Giannakakis, A, Zhang, J, Jenjaroenpun, P, Nama, S, Zainolabidin, N, Aau, M.Y, Yarmishyn, A.A, Vaz, C, Ivshina, A.V, Grinchuk, O.V, Voorhoeve, M, Vardy, L.A, Sampath, P, Kuznetsov, V.A, Kurochkin, I.V, Guccione, E (2015). Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress. Scientific Reports 5 : 9737. ScholarBank@NUS Repository.
Abstract: 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-regulated, this novel divergent, PolII pausing-phenomenon leads to the generation of thousands of long noncoding RNAs (lncRNAs) with promoter-associated antisense lncRNAs transcripts (si-paancRNAs) representing the major group of stress-induced transcripts. OS causes transient dynamics of si-lncRNAs in nucleus and cytosol, leading to their accumulation at polysomes, in contrast to mRNAs, which get depleted from polysomes. We propose that si-lncRNAs represent a novel component of the transcriptional stress that is known to determine the outcome of immediate-early and later cellular stress responses and we provide insights on the fate of those novel mature lncRNA transcripts by showing that their association with polysomal complexes is significantly increased in OS.
Source Title: Scientific Reports
ISSN: 2045-2322
DOI: 10.1038/srep09737
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