scholarly journals An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis

2021 ◽  
Vol 7 (1) ◽  
pp. eabd4722
Author(s):  
Juan Perianez-Rodriguez ◽  
Marcos Rodriguez ◽  
Marco Marconi ◽  
Estefano Bustillo-Avendaño ◽  
Guy Wachsman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Primary Root ◽  
Biological Clock ◽  
Periodic Pattern ◽  
Oscillatory Circuit ◽  
Lateral Organs ◽  
Exogenous Cues ◽  
Model Predictions ◽  
Regulatory Loop ◽  
External Stimuli

In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression. The core molecular mechanism that drives the root clock periodicity and how it is modified by exogenous cues such as auxin and gravity remain unknown. We identified the key elements of the oscillator (AUXIN RESPONSE FACTOR 7, its auxin-sensitive inhibitor IAA18/POTENT, and auxin) that form a negative regulatory loop circuit in the oscillation zone. Through multilevel computer modeling fitted to experimental data, we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. Furthermore, gravistimulation experiments based on the model predictions show that external auxin stimuli can lead to entrainment of the root clock. Our work demonstrates the mechanism underlying a robust biological clock and how it can respond to external stimuli.

The dominant hemimelia mutation uncouples epithelial-mesenchymal interactions and disrupts anterior mesenchyme formation in mouse hindlimbs

Development ◽  
1999 ◽  
Vol 126 (21) ◽  
pp. 4729-4736
Author(s):  
L. Lettice ◽  
J. Hecksher-Sorensen ◽  
R.E. Hill
Keyword(s):  
Gene Expression ◽  
Pattern Formation ◽  
Limb Development ◽  
Limb Bud ◽  
Mouse Mutation ◽  
Number Of Factors ◽  
Limb Outgrowth ◽  
Gene Functions ◽  
Regulatory Loop ◽  
Limb Initiation

Epithelial-mesenchymal interactions are essential for both limb outgrowth and pattern formation in the limb. Molecules capable of communication between these two tissues are known and include the signaling molecules SHH and FGF4, FGF8 and FGF10. Evidence suggests that the pattern and maintenance of expression of these genes are dependent on a number of factors including regulatory loops between genes expressed in the AER and those in the underlying mesenchyme. We show here that the mouse mutation dominant hemimelia (Dh) alters the pattern of gene expression in the AER such that Fgf4, which is normally expressed in a posterior domain, and Fgf8, which is expressed throughout are expressed in anterior patterns. We show that maintenance of Shh expression in the posterior mesenchyme is not dependent on either expression of Fgf4 or normal levels of Fgf8 in the overlying AER. Conversely, AER expression of Fgf4 is not directly dependent on Shh expression. Also the reciprocal regulatory loop proposed for Fgf8 in the AER and Fgf10 in the underlying mesenchyme is also uncoupled by this mutation. Early during the process of limb initiation, Dh is involved in regulating the width of the limb bud, the mutation resulting in selective loss of anterior mesenchyme. The Dh gene functions in the initial stages of limb development and we suggest that these initial roles are linked to mechanisms that pattern gene expression in the AER.

The chiaroscuro stem cell: a unified stem cell theory

Blood ◽  
2002 ◽  
Vol 100 (13) ◽  
pp. 4266-4271 ◽  
Author(s):  
Peter J. Quesenberry ◽  
Gerald A. Colvin ◽  
Jean-Francois Lambert
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Stem Cell ◽  
Marrow Cell ◽  
Receptor Expression ◽  
Cell Theory ◽  
Surface Receptor ◽  
Stem Cell Hierarchy ◽  
External Stimuli ◽  
Existing Data

Hematopoiesis has been considered hierarchical in nature, but recent data suggest that the system is not hierarchical and is, in fact, quite functionally plastic. Existing data indicate that engraftment and progenitor phenotypes vary inversely with cell cycle transit and that gene expression also varies widely. These observations suggest that there is no progenitor/stem cell hierarchy, but rather a reversible continuum. This may, in turn, be dependent on shifting chromatin and gene expression with cell cycle transit. If the phenotype of these primitive marrow cells changes from engraftable stem cell to progenitor and back to engraftable stem cell with cycle transit, then this suggests that the identity of the engraftable stem cell may be partially masked in nonsynchronized marrow cell populations. A general model indicates a marrow cell that can continually change its surface receptor expression and thus responds to external stimuli differently at different points in the cell cycle.

scholarly journals The Role of Endogenous Carbon Monoxide (CO) in the Functioning of Biological Clocks in Pig and Wild Boar Hybrids During Long- and Short-day Seasons

2021 ◽  
Author(s):  
Przemysław GILUN ◽  
Barbara Wąsowska ◽  
Magdalena Sowa-Kućma ◽  
Katarzyna Kozioł ◽  
Maria Romerowicz-Misielak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Wild Boar ◽  
Clock Genes ◽  
Autologous Blood ◽  
Biological Clock ◽  
Biological Clocks ◽  
Light Emitting ◽  
Short Day ◽  
The Right ◽  
Induced Changes

Abstract Mature males of a wild boar-pig crossbreed during long- and short-day seasons were used for the study, which demonstrated that the chemical light carrier CO regulates the expression of biological clock genes in the hypothalamus (preoptic area - POA and dorsal part of hypothalamus - DH) via humoral pathways. Autologous blood with experimentally elevated concentrations of endogenous CO (using lamps with white light-emitting diodes) was infused into the ophthalmic venous sinus via the right dorsal nasal vein.The results showed that elevated endogenous CO levels through blood irradiation induced changes in gene expression involved in the functioning of the main biological clock. Changes in the expression of the transcription factors Bmal1, Clock and Npas2 had a similar pattern in both structures, where a very large decrease in gene expression was shown after exposure to elevated endogenous CO levels. The changes in the gene expression of PER 1-2, CRY 1-2, REV-ERB α-β and ROR β are not the same for both POA and DH hypothalamic structures, indicating that both structures respond differently to the received humoral signal.The obtained results indicate that CO is a chemical light molecule whose production in organisms depends on the amount of light. An adequate amount of light is an essential factor for the proper functioning of the main biological clock.

scholarly journals Effect of acute noise trauma on the gene expression profile of the hippocampus

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Chang Ho Lee ◽  
Kyung Woon Kim ◽  
So Min Lee ◽  
So Young Kim
Keyword(s):  
Gene Expression ◽  
Noise Exposure ◽  
Control Group ◽  
Sprague Dawley ◽  
Qrt Pcr ◽  
Neuronal Systems ◽  
Immune Related Genes ◽  
Pathway Analyses ◽  
Upregulated Genes ◽  
External Stimuli

Abstract Background This study aimed to investigate the changes in the expression of hippocampal genes upon acute noise exposure. Methods Three-week-old Sprague–Dawley rats were assigned to control (n = 15) and noise (n = 15) groups. White noise (2–20 kHz, 115 dB sound pressure level [SPL]) was delivered for 4 h per day for 3 days to the noise group. All rats were sacrificed on the last day of noise exposure, and gene expression in the hippocampus was analyzed using a microarray. Pathway analyses were conducted for genes that showed differential expression ≥ 1.5-fold and P ≤ 0.05 compared to the control group. The genes included in the putative pathways were measured using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Results Thirty-eight upregulated genes and 81 downregulated genes were identified. The pathway analyses revealed that upregulated genes were involved in the cellular responses to external stimuli and immune system pathways. qRT-PCR confirmed the upregulation of the involved genes. The downregulated genes were involved in neuronal systems and synapse-related pathways, and qRT-PCR confirmed the downregulation of the involved genes. Conclusions Acute noise exposure upregulated the expression of immune-related genes and downregulated the expression of neurotransmission-related genes in the hippocampus.

scholarly journals Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell

2020 ◽  
Vol 21 (21) ◽  
pp. 8278
Author(s):  
Amparo Pascual-Ahuir ◽  
Josep Fita-Torró ◽  
Markus Proft
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Transient Gene Expression ◽  
Cell Physiology ◽  
Extrinsic Factors ◽  
Intrinsic Factors ◽  
Gene Expression Dynamics ◽  
Transcriptional Memory ◽  
External Stimuli

The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.

scholarly journals Polysome arrest restricts miRNA turnover by preventing exosomal export of miRNA in growth-retarded mammalian cells

2015 ◽  
Vol 26 (6) ◽  
pp. 1072-1083 ◽  
Author(s):  
Souvik Ghosh ◽  
Mainak Bose ◽  
Anirban Ray ◽  
Suvendra N. Bhattacharyya
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Cell Growth ◽  
Subcellular Distribution ◽  
Mammalian Cells ◽  
Cellular Response ◽  
Mature Mirnas ◽  
Regulatory Rnas ◽  
The Stability ◽  
External Stimuli

MicroRNAs (miRNAs) are tiny posttranscriptional regulators of gene expression in metazoan cells, where activity and abundance of miRNAs are tightly controlled. Regulated turnover of these regulatory RNAs is important to optimize cellular response to external stimuli. We report that the stability of mature miRNAs increases inversely with cell proliferation, and the increased number of microribonucleoproteins (miRNPs) in growth-restricted mammalian cells are in turn associated with polysomes. This heightened association of miRNA with polysomes also elicits reduced degradation of target mRNAs and impaired extracellular export of miRNA via exosomes. Overall polysome sequestration contributes to an increase of cellular miRNA levels but without an increase in miRNA activity. Therefore miRNA activity and turnover can be controlled by subcellular distribution of miRNPs that may get differentially regulated as a function of cell growth in mammalian cells.

scholarly journals Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

2020 ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Target Genes ◽  
Intron Retention ◽  
Single Gene ◽  
Exon Skipping ◽  
Environmental Response ◽  
Biotic Stresses ◽  
External Stimuli

AbstractBackgroundAlternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing.ResultsWe generated a massive resource for A. thaliana (PastDB; pastdb.crg.eu), comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets revealed that A. thaliana shows high levels of AS (similar to fruitflies) and that, compared to animals, disproportionately uses AS for stress responses. We identified core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that was tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, were overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion.ConclusionsNon-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

scholarly journals Simultaneous Monitoring of Behavior & Peripheral Clocks in Drosophila Reveals Unstructured Sleep in an Alzheimer's Model

2015 ◽  
Author(s):  
Eleonora Khabirova ◽  
Ko-Fan Chen ◽  
John S O'Neill ◽  
Damian C Crowther
Keyword(s):  
Gene Expression ◽  
Clock Gene ◽  
Biological Clock ◽  
Model Organisms ◽  
Clock Gene Expression ◽  
Biological Phenomena ◽  
Model Of Alzheimer’S Disease ◽  
Sleep Homeostasis ◽  
Regulatory Machinery ◽  
Activity Cycles

Sleep and circadian rhythms are ancient, related biological phenomena controlled by distinct neuronal circuits, whose appropriate regulation is critical for health. Whereas the regulatory machinery underlying sleep homeostasis is ill-defined, the biological clock mechanism is better understood: from cell-intrinsic feedback loops of ‘clock gene’ expression to circuits that facilitate rhythmic behavior. Age- and neurodegeneration related deterioration in sleep/wake timing was first described in humans decades ago, but has only recently been recapitulated in model organisms. In order to delineate the causal relationships between aging, sleep, neuronal function and the molecular clockwork, we have developed FLYGLOW, a broadly applicable bioluminescence-based system which allows rest/activity cycles, sleep consolidation and molecular clock gene expression to be quantified simultaneously in dozens of individual flies over many days/weeks. We show that FLYGLOW outperforms existing methods, and demonstrate the utility of the multiparameter correlational analyses within and between flies that it enables. We go on to show unambiguously that peripheral cellular rhythms can free-run independently of the central pacemakers that drive behavioural cycles. Finally, using a fly model of Alzheimer’s disease (AD) we observe a profound disorganization of sleep and activity cycles, that phenocopies the human disease.

scholarly journals Stochasticity and negative feedback lead to pulsed dynamics and distinct gene activity patterns

2014 ◽  
Author(s):  
Samuel Zambrano ◽  
Marco E. Bianchi ◽  
Alessandra Agresti ◽  
Nacho Molina
Keyword(s):  
Gene Expression ◽  
Stochastic Process ◽  
Simple Model ◽  
Negative Feedback ◽  
Regulatory Network ◽  
Activity Patterns ◽  
Hybrid Modelling ◽  
Regulatory Loop ◽  
Gene Switching ◽  
Modelling Approach

Gene expression is an inherently stochastic process that depends on the structure of the biochemical regulatory network in which the gene is embedded. Here we study the interplay between stochastic gene switching and the widespread negative feedback regulatory loop. Using a simple hybrid model, we find that stochasticity in gene switching by itself can induce pulses in the system. Furthermore, we find that our simple model is able to reproduce both exponential and peaked distributions of gene active and inactive times similar to those that have been observed experimentally. Our hybrid modelling approach also allows us to link these patterns to the dynamics of the system for each gene state.

Neurospora crassa clock-controlled genes are regulated at the level of transcription

1991 ◽  
Vol 11 (1) ◽  
pp. 558-563
Author(s):  
J J Loros ◽  
J C Dunlap
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Circadian Rhythm ◽  
Neurospora Crassa ◽  
Regulatory Networks ◽  
Biological Clock ◽  
Transcriptional Analysis ◽  
Biological Processes ◽  
Control Of Gene Expression ◽  
A Cell

Although an extensive number of biological processes are under the daily control of the circadian biological clock, little is known about how the clock maintains its regulatory networks within a cell. An important aspect of this temporal control is the daily control of gene expression. Previously we identified two morning-specific genes that are regulated by the clock through daily control of gene expression (J. Loros, S. Denome, and J.C. Dunlap, Science 243:385-388, 1989). We have now introduced a method for transcriptional analysis in Neurospora crassa and used this nuclear run-on procedure to show that regulation of mRNA abundance for these two morning-specific genes occurs at the level of transcription. This transcriptional regulation by the circadian clock provides a basis for isolating circadian rhythm mutants.

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