Ontology highlight
ABSTRACT:
PROVIDER: PRJNA113675 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptional responses to stimuli are regulated by tuning rates of transcript production and degradation. Here we show that stimulation-induced changes in transcript production and degradation rates can be inferred from simultaneously measured precursor mRNA (pre-mRNA) and mature mRNA profiles. Our studies on the transcriptome-wide responses to extracellular stimuli in different cellular model systems revealed hitherto unanticipated dynamics of transcript production and degradation rates. Intriguingly, genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production. Moreover, we identify a group of genes, which take advantage of the unexpectedly large dynamic range of production rates to expedite their induction by a transient production overshoot. These findings provide an unprecedented quantitative view on processes governing transcriptional responses, and may have broad implications for understanding their regulation at the transcriptional and post-transcriptional levels. MCF10A cells stimulated with EGF
2011-08-30 | E-GEOD-24391 | biostudies-arrayexpress
Project description:Transcriptional responses to stimuli are regulated by tuning rates of transcript production and degradation. Here we show that stimulation-induced changes in transcript production and degradation rates can be inferred from simultaneously measured precursor mRNA (pre-mRNA) and mature mRNA profiles. Our studies on the transcriptome-wide responses to extracellular stimuli in different cellular model systems revealed hitherto unanticipated dynamics of transcript production and degradation rates. Intriguingly, genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production. Moreover, we identify a group of genes, which take advantage of the unexpectedly large dynamic range of production rates to expedite their induction by a transient production overshoot. These findings provide an unprecedented quantitative view on processes governing transcriptional responses, and may have broad implications for understanding their regulation at the transcriptional and post-transcriptional levels. MCF10A cells stimulated with EGF, DEX, and their combination
2014-08-30 | E-GEOD-53405 | biostudies-arrayexpress
Project description:Transcriptional responses to stimuli are regulated by tuning rates of transcript production and degradation. Here we show that stimulation-induced changes in transcript production and degradation rates can be inferred from simultaneously measured precursor mRNA (pre-mRNA) and mature mRNA profiles. Our studies on the transcriptome-wide responses to extracellular stimuli in different cellular model systems revealed hitherto unanticipated dynamics of transcript production and degradation rates. Intriguingly, genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production. Moreover, we identify a group of genes, which take advantage of the unexpectedly large dynamic range of production rates to expedite their induction by a transient production overshoot. These findings provide an unprecedented quantitative view on processes governing transcriptional responses, and may have broad implications for understanding their regulation at the transcriptional and post-transcriptional levels.
2014-08-30 | GSE53405 | GEO
Project description:Transcriptional responses to stimuli are regulated by tuning rates of transcript production and degradation. Here we show that stimulation-induced changes in transcript production and degradation rates can be inferred from simultaneously measured precursor mRNA (pre-mRNA) and mature mRNA profiles. Our studies on the transcriptome-wide responses to extracellular stimuli in different cellular model systems revealed hitherto unanticipated dynamics of transcript production and degradation rates. Intriguingly, genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production. Moreover, we identify a group of genes, which take advantage of the unexpectedly large dynamic range of production rates to expedite their induction by a transient production overshoot. These findings provide an unprecedented quantitative view on processes governing transcriptional responses, and may have broad implications for understanding their regulation at the transcriptional and post-transcriptional levels.
2011-08-31 | GSE24391 | GEO
Project description:We subjected yeast to two stresses, oxidative stress, which under current settings induces a fast and transient response in mRNA abundance, and DNA damage, which triggers a slow enduring response. Using microarrays, we performed a transcriptional arrest experiment to measure genome-wide mRNA decay profiles under each condition. Genome-wide decay kinetics in each condition were compared to decay experiments that were performed in a reference condition (only transcription inhibition without an additional stress) to quantify changes in mRNA stability in each condition. We found condition-specific changes in mRNA decay rates and coordination between mRNA production and degradation. In the transient response, most induced genes were surprisingly destabilized, while repressed genes were somewhat stabilized, exhibiting counteraction between production and degradation. This strategy can reconcile high steady-state level with short response time among induced genes. In contrast, the stress that induces the slow response displays the more expected behavior, whereby most induced genes are stabilized, and repressed genes destabilized. Our results show genome-wide interplay between mRNA production and degradation, and that alternative modes of such interplay determine the kinetics of the transcriptome in response to stress. Experiment Overall Design: We used Affymetrix microarrays to measure the decay profiles of all genes following transcription inhibition in four separate experiments. In two reference experiments, only transcription inhibtion was applied. In two other experiments, an additional stress was applied prior to transcription inhibition: oxidative stress (0.3mM hydrogen peroxide) or DNA damage (0.1% methyl methanesulfonate).
2008-10-26 | E-GEOD-12221 | biostudies-arrayexpress
Project description:We subjected yeast to two stresses, oxidative stress, which under current settings induces a fast and transient response in mRNA abundance, and DNA damage, which triggers a slow enduring response. Using microarrays, we performed a transcriptional arrest experiment to measure genome-wide mRNA decay profiles under each condition. Genome-wide decay kinetics in each condition were compared to decay experiments that were performed in a reference condition (only transcription inhibition without an additional stress) to quantify changes in mRNA stability in each condition. We found condition-specific changes in mRNA decay rates and coordination between mRNA production and degradation. In the transient response, most induced genes were surprisingly destabilized, while repressed genes were somewhat stabilized, exhibiting counteraction between production and degradation. This strategy can reconcile high steady-state level with short response time among induced genes. In contrast, the stress that induces the slow response displays the more expected behavior, whereby most induced genes are stabilized, and repressed genes destabilized. Our results show genome-wide interplay between mRNA production and degradation, and that alternative modes of such interplay determine the kinetics of the transcriptome in response to stress. Keywords: Four separate time courses
2008-10-01 | GSE12221 | GEO
Project description:In malaria parasites, the regulation of mRNA translation, storage and degradation during development and life stage transitions remains largely unknown. Here, we functionally characterized the DEAD-box RNA helicase PfDOZI in P. falciparum. Disruption of pfdozi enhanced asexual proliferation but reduced sexual commitment and impaired gametocyte development. By quantitative transcriptomics, we show that PfDOZI is involved in the regulation of invasion-related genes and sexual stage-specific genes during different developmental stages. PfDOZI predominantly participates in processing body-like mRNPs in schizonts but germ cell granule-like mRNPs in gametocytes to impose opposing actions of degradation and protection on different mRNA targets. We further show the formation of stress granule-like mRNPs during nutritional deprivation, highlighting an essential role of PfDOZI-associated mRNPs in stress response. Here, we demonstrate that PfDOZI participates in distinct mRNPs to maintain mRNA homeostasis in response to life-stage transition and environmental changes by differentially executing post-transcriptional regulation on the target mRNAs.
2024-04-30 | PXD051782 | Pride
Project description:LlorénsRico2016 - Effects of cis-Encoded
antisense RNAs (asRNAs) - Case1
Three
putative effects of the asRNAs were considered in this study: in
case 1
,
the binding of the asRNA to the corresponding mRNA induces
degradation of the duplex. In case 2
(this
model)
the binding of the asRNA to the mRNA induces degradation of the
mRNA, but not of the asRNA. In case 3, the mRNA and the asRNA
bind reversibly to form a stable duplex, preventing translation
of the mRNA. In all the three cases, binding to the ribosome
protects the mRNA from the effect of the asRNA.
This model is described in the article:
Bacterial antisense RNAs are
mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J,
Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano
L, Lluch-Senar M.
Sci Adv 2016 Mar; 2(3): e1501363
Abstract:
cis-Encoded antisense RNAs (asRNAs) are widespread along
bacterial transcriptomes. However, the role of most 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 nine different asRNAs in Mycoplasma 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.
This model is hosted on
BioModels Database
and identified by:
MODEL1511170001.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1511170001 | BioModels
Project description:LlorénsRico2016 - Effects of cis-Encoded
antisense RNAs (asRNAs) - Case3
Three putative
effects of the asRNAs were considered in this study: in case 1,
the binding of the asRNA to the corresponding mRNA induces
degradation of the duplex. In case 2, the binding of the asRNA
to the mRNA induces degradation of the mRNA, but not of the
asRNA. In case 3 (this model), the mRNA and the asRNA bind
reversibly to form a stable duplex, preventing translation of
the mRNA. In all the three cases, binding to the ribosome
protects the mRNA from the effect of the asRNA.
This model is described in the article:
Bacterial antisense RNAs are
mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J,
Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano
L, Lluch-Senar M.
Sci Adv 2016 Mar; 2(3): e1501363
Abstract:
cis-Encoded antisense RNAs (asRNAs) are widespread along
bacterial transcriptomes. However, the role of most 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 nine different asRNAs in Mycoplasma 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.
This model is hosted on
BioModels Database
and identified by:
MODEL1511170002.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1511170002 | BioModels
Project description:LlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1
Three
putative effects of the asRNAs were considered in this study: in
case 1
(this
model)
,
the binding of the asRNA to the corresponding mRNA induces
degradation of the duplex. In case 2, the binding of the asRNA to
the mRNA induces degradation of the mRNA, but not of the asRNA.
In case 3, the mRNA and the asRNA bind reversibly to form a
stable duplex, preventing translation of the mRNA. In all the
three cases, binding to the ribosome protects the mRNA from the
effect of the asRNA.
This model is described in the article:
Bacterial antisense RNAs are
mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J,
Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano
L, Lluch-Senar M.
Sci Adv 2016 Mar; 2(3): e1501363
Abstract:
cis-Encoded antisense RNAs (asRNAs) are widespread along
bacterial transcriptomes. However, the role of most 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 nine different asRNAs in Mycoplasma 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.
This model is hosted on
BioModels Database
and identified by:
MODEL1511170000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1511170000 | BioModels