Index of papers in April 2015 that mention
  • mRNA
Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana
Abstract
Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3’UTR, a region affecting mRNA translation, localization and stability.
Author Summary
ORFs With peaks have decreased mRNA stability and prevalent regulatory functions.
Flexibility peaks are conserved and identify genes with decreased mRNA stability
Flexibility peaks are conserved and identify genes with decreased mRNA stability
Flexibility peaks are conserved and identify genes with decreased mRNA stability
The 3’UTR regulates mRNA levels or stability via RNA-protein interactions with mRNA degradation machinery.
Flexibility peaks are conserved and identify genes with decreased mRNA stability
mRNA stability is a key regulatory step controlling gene eXpression and ultimately affects protein levels and function.
Flexibility peaks map on polyadenylation signals
The BB promotes the recruitment of other polyadenylation factors by binding, upon transcription of RNA, the transacting factor H rpl, that also plays important roles in mRNA export, mRNA surveillance and nonsense mediated decay.
mRNA is mentioned in 16 sentences in this paper.
Topics mentioned in this paper:
Stuart Aitken, Shigeyuki Magi, Ahmad M. N. Alhendi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. Semple , the FANTOM Consortium
Discovery of non-coding RNA genes active in the immediate-early response
Many mRNA are repressed by more than one ID-miR, for example, EGR1 is targeted by hsa-mir- 191 and hsa-mir-212.
Discovery of non-coding RNA genes active in the immediate-early response
Reasoning that miRNA-mediated repression will be reflected in the CAGE signals, either by direct action on mRNA or indirectly through transcriptional inactivation processes, we sought to establish a connection between the targets of mature miRNA that are assigned to the dip signature, and protein-coding genes with CAGE clusters assigned to the early peak signature in MCF7 cells stimulated with HRG.
Discussion
Such similarities and differences between the epigenetic regulation of lncRNA and mRNA have been reported previously in genome-wide data [17].
Introduction
Studies of IEG induction show distinct differences between the kinetics of pre-mRNA and mature mRNA which are particularly evident for delayed IEGs where the mature mRNA may peak up to 3 hours later than the precursor [6].
Introduction
A transient overshoot in pre-mRNA production has been proposed as a strategy to shape the timing and magnitude of response in the face of the slow mRNA degradation kinetics that would otherwise determine the kinetics [9].
Introduction
Recent studies have implicated splicing as an important factor controlling IEG expression, such that the F08 locus can remain transcriptionally active long after spliced mRNA production has ceased [11].
Kinetics and chromatin features underlying IEG induction
This may indicate that the (pre) mRNA kinetics of switch-ing-on are faster than switch-off kinetics as might be expected due to the latter being dominated by relatively slow mRNA degradation rates in many cases [9].
Results
These patterns were intended to capture mRNA transcription in response to a stimulus.
Results
Such eXponential kinetics are characteristic of formalised systems biology models (comparable With observed and modelled mRNA and pre-mRNA eXpression in [4, 9]), and may reflect changes in both transcription and degradation rates over time [20].
mRNA is mentioned in 12 sentences in this paper.
Topics mentioned in this paper:
Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff
Abstract
Bursting transcription can cause individual cells to remain in synchrony transiently, offering an explanation of transcriptional cycling as observed in cell populations, both on promoter chromatin status and mRNA levels.
Author Summary
Transcription initiation is an important process that contributes to determining mRNA and eventually protein levels.
Author Summary
In the ratchet model, one particular chromatin state allows for RNA polymerase rebinding, which makes bursts in mRNA production a basic feature of the ratchet mechanism.
Bursts in the system
Many experimental studies have shown that mRNA is produced in bursts [14, 54—56] of variable size [57, 58].
Bursts in the system
This finding is in good agreement with experimental observations that mRNA burst-size distributions for regulated genes across a cell population are often geometric [54, 55].
Bursts in the system
Fig 5C and 5D show the prediction of mRNA trajectories in five individual cells for the 9-state ratchet cycle model that were induced at the same time (Fig 4A).
Experimental evidence for the ticking mechanism
This is the state during which RNA po-lymerases are assembled into ranscriptionally competent complexes, and start the elongation of an mRNA transcript.
Introduction
Despite many recent experimental studies, we lack a realistic, dynamic picture of transcription initiation that integrates time scales of nucleosome modifications, protein complex formation, RNA polymerase assembly and its escape from regulatory regions, mRNA elongation and mRNA-concentration dynamics.
mRNA is mentioned in 18 sentences in this paper.
Topics mentioned in this paper:
Thomas W. Spiesser, Clemens Kühn, Marcus Krantz, Edda Klipp
Abstract
Moreover, we assess the impact of the observed bud-localisation of the G2 cyclin CLB2 mRNA , and find that localised cyclin translation could provide an efficient mechanism for measuring the biosynthetic capacity in specific compartments: The mother in G1, and the growing bud in G2.
Abstract
Size control seems to be exerted twice, where the Gg/M control affects bud size through bud-localized translation of CLB2 mRNA , explaining the dependence of the S-G2-M duration on nutrients.
Discussion
The importance of the mRNA localisation, as we highlight it here, can possibly be tested experimentally.
Discussion
The polarised localisation of mCLBZ could be perturbed by disruption of the sequence in mCLBZ required for transport (if identified), or by deletion of the M YO4 gene that encodes the type V myosin motor responsible for bud-localisation of mRNA [56].
Introduction
Intriguingly, CLBZ mRNA (mCLBZ) accumulates in the bud, while the Clb2 protein is distributed throughout the cell [35, 36].
Introduction
In principle, active transport of the mRNA leading to lo-calised translation of mCLBZ could serve to measure the biosynthetic capacity of the bud, to form a bud (daughter) sizer in G2.
Results
In Model-2, the mRNA is translated exclusively in the newly forming bud mimicking the effect of mRNA localization.
The model
Assuming that the important function of mCLBZ transport into the bud is to localise translation to this sub compartment, we allowed only the fraction of ribosomes in the bud to translate the CLB mRNA .
mCLB localization reduces noise at mitotic entry to stabilise cell size
To further distinguish the models, we analysed the effect of mRNA localization on other systems level properties beyond average size and cell cycle phase duration.
mRNA is mentioned in 9 sentences in this paper.
Topics mentioned in this paper: