Antisense transcription and its roles in response to environmental changes in E. coli K12
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli K-12
PROVIDER: GSE64021 | GEO | 2023/12/15
REPOSITORIES: GEO
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Project description:cis-antisense RNAs (cis-asRNAs) in prokaryotes are more pervasive than originally thought. However, little is known about their expression patterns and functions. Here we determined transcriptomes and proteomes of E. coli at multiple time points in five culture conditions using directional RNA-seq and tandem mass spectrometry. We found that a highly varying portion (27.2%~90.8%) of transcribed genes had cis-asRNAs dependent on growth phases and culture conditions, and that almost all transcribed genes changed their cis-asRNA levels relative to the mRNA level at different growth phases and culture conditions. Intriguingly, the correlation between the protein and mRNA levels of genes is abolished the increasing cis-asRNA levels relative to the mRNA levels, suggesting that cis-asRNAs might directly or indirectly inhibit translation by forming duplexes with mRNAs. All data sets are available for data mining from a unified resource to support further biological discoveries and insights into cis-asRNA-mediated gene expressional regulation.
2022-02-28 | PXD001640 | Pride
Project description:Antisense RNAs (asRNAs) have diverse functions across three superkingdoms of life. However, their physiological roles for photosynthesis, the most efficient conversion system of solar energy and carbon dioxide into desirable biofuel, are elusive. To understand asRNA-mediated photosynthetic response, we systematically identified non-coding asRNAs and analyzed their differential regulation upon high light and/or low temperature. We found that large fractions of antisense regions are pervasively transcribed and differentially induced upon the change of light and/or temperature. Particularly, photosynthesis and ribosome related genes are mostly regulated by asRNA. Futhermore, we found that 93 long non-coding asRNAs spanning more than half of the cognate open reading frames (ORFs), unexpectedly. Intriguingly, many of them are associated with photosynthetic genes and they have positive role to the expression level of their cognate ORFs. Thus, our systematic transcriptome analysis of photosynthetic response indicates that asRNAs may finetune transcriptional response to enable efficient photosynthetic energy conversion.
2020-07-25 | GSE60109 | GEO
Project description:Cis-encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of the vast majority of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content, and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing 9 different asRNAs in M. pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.
2018-10-25 | PXD003231 | Pride
Project description:Cis-encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of the vast majority of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content, and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing 9 different asRNAs in M. pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.
2016-01-18 | E-MTAB-4081 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE41936: Rho and NusG suppress pervasive antisense transcription in Escherichia coli [ChIP-chip]. GSE41938: Rho and NusG suppress pervasive antisense transcription in Escherichia coli [tiling array]. GSE41939: Rho and NusG suppress pervasive antisense transcription in Escherichia coli [RNA-seq]. Refer to individual Series
2012-11-01 | E-GEOD-41940 | biostudies-arrayexpress
Project description:The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey on the number and types of antisense (as)RNAs. A tiled microarray was constructed with probes for both strands of the genes or intergenic spacers with candidate transcripts predicted by an algorithm and an equally sized and distributed control set. The resulting 102,739 individual probes cover an accumulated length of 1,441,146 nt or about 40% of the total chromosome sequence of Synechocystis 6803. Hybridization of this array with total RNA isolated from cultures raised under different growth conditions identified a high number of transcripts from intergenic spacers and in antisense orientation to known genes (natural cis-asRNAs). Extrapolated to the whole genome, around 10% of all open reading frames in Synechocystis 6803 may have a corresponding asRNA, suggesting a much more important role of chromosomally encoded asRNAs in bacteria then anticipated so far. Keywords: stress response
2009-01-14 | GSE14410 | GEO
Project description:The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey on the number and types of antisense (as)RNAs. A tiled microarray was constructed with probes for both strands of the genes or intergenic spacers with candidate transcripts predicted by an algorithm and an equally sized and distributed control set. The resulting 102,739 individual probes cover an accumulated length of 1,441,146 nt or about 40% of the total chromosome sequence of Synechocystis 6803. Hybridization of this array with total RNA isolated from cultures raised under different growth conditions identified a high number of transcripts from intergenic spacers and in antisense orientation to known genes (natural cis-asRNAs). Extrapolated to the whole genome, around 10% of all open reading frames in Synechocystis 6803 may have a corresponding asRNA, suggesting a much more important role of chromosomally encoded asRNAs in bacteria then anticipated so far. Keywords: stress response 4 RNA hybridizations, 2 DNA controls. The raw data from the DNA hybridizations are in the GSE14410_DNA_1.txt and GSE14410_DNA_2.txt files.
2010-05-14 | E-GEOD-14410 | biostudies-arrayexpress
Project description:Pervasive transcription generates mainly unstable non-coding transcripts. Although a few examples of pervasive antisense have been shown to mediate gene regulation by transcriptional interference, whether pervasive transcription has a general functional role or merely represents transcriptional noise remains to be determined. In a mutant context that revealed pervasive transcripts, we characterized more than 800 antisenses genome wide and analysed the corresponding sense mRNA behaviour. We observed that antisense non-coding transcription is commonly found associated with genes tightly repressed during the exponential phase with an opposite level of mRNA and the associated antisense. This suggested that antisense transcription might participate to a tight repression of genes during the exponential phase. We thus specifically interrupted the antisense transcription of a subset of genes, and found that it resulted in a de-repression of the corresponding mRNAs. We further validated that this repression acts in cis through a transcriptional interference mechanism, which involves several chromatin modification factors. Transcription interference is observed for the first time as a general mean of gene regulation between cellular states.
2018-07-23 | GSE101368 | GEO
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