scholarly journals Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

2018 ◽  
Author(s):  
Augusto Berrocal ◽  
Nicholas Lammers ◽  
Hernan G. Garcia ◽  
Michael B. Eisen
Keyword(s):  
Drosophila Melanogaster ◽  
Pattern Formation ◽  
Transcriptional Activity ◽  
High Temporal Resolution ◽  
Burst Frequency ◽  
Computational Framework ◽  
Developmental Patterns ◽  
Transcriptional Dynamics ◽  
Transcriptional Bursting ◽  
Over Time

AbstractWe used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its seven stripe expression pattern forms, and developed tools to characterize and visualize how transcriptional bursting varies over time and space. We find that despite being created by the independent activity of five enhancers, even-skipped stripes are sculpted by the same kinetic phenomena: a coupled increase of burst frequency and amplitude. By tracking the position and activity of individual nuclei, we show that stripe movement is driven by the exchange of bursting nuclei from the posterior to anterior stripe flanks. Our work provides a conceptual, theoretical and computational framework for dissecting pattern formation in space and time, and reveals how the coordinated transcriptional activity of individual nuclei shape complex developmental patterns.

scholarly journals Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Augusto Berrocal ◽  
Nicholas C Lammers ◽  
Hernan G Garcia ◽  
Michael B Eisen
Keyword(s):  
Drosophila Melanogaster ◽  
Pattern Formation ◽  
Transcriptional Activity ◽  
High Temporal Resolution ◽  
Burst Frequency ◽  
Computational Framework ◽  
Developmental Patterns ◽  
Transcriptional Dynamics ◽  
Transcriptional Bursting ◽  
Over Time

We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its seven stripe expression pattern forms, and developed tools to characterize and visualize how transcriptional bursting varies over time and space. We find that despite being created by the independent activity of five enhancers, even-skipped stripes are sculpted by the same kinetic phenomena: a coupled increase of burst frequency and amplitude. By tracking the position and activity of individual nuclei, we show that stripe movement is driven by the exchange of bursting nuclei from the posterior to anterior stripe flanks. Our work provides a conceptual, theoretical and computational framework for dissecting pattern formation in space and time, and reveals how the coordinated transcriptional activity of individual nuclei shape complex developmental patterns.

scholarly journals Transcriptional kinetics and molecular functions of long non-coding RNAs

2020 ◽  
Author(s):  
Per Johnsson ◽  
Christoph Ziegenhain ◽  
Leonard Hartmanis ◽  
Gert-Jan Hendriks ◽  
Michael Hagemann-Jensen ◽  
...  
Keyword(s):  
Cell Cycle Progression ◽  
Burst Frequency ◽  
Protein Coding ◽  
Rna Molecules ◽  
Transcriptional Dynamics ◽  
Long Duration ◽  
Non Coding Rnas ◽  
Transcriptional Bursting ◽  
Regulatory Functions ◽  
Cell To Cell Variability

AbstractAn increasing number of studies have demonstrated the regulatory importance of long non-coding RNAs (lncRNAs), yet little is known about their transcriptional dynamics and it remains challenging to determine their regulatory functions. Here, we used allele-sensitive single-cell RNA-seq (scRNA-seq) to demonstrate that lncRNAs have lower burst frequencies with twice as long duration between bursts, compared to mRNAs. Additionally, we observed an increased cell-to-cell variability in lncRNA expression that was due to more sporadic bursting (lower frequency) with larger numbers of RNA molecules being produced. Exploiting heterogeneity in asynchronously growing cells, we identified and experimentally validated lncRNAs with cell-state specific functions involved in cell cycle progression and apoptosis. Finally, utilizing allele-resolved RNA expression, we identified cis functioning lncRNAs and observed that knockdown of these lncRNAs modulated either transcriptional burst frequency or size of the nearby protein-coding gene. Collectively, our results identify distinct transcriptional regulation of lncRNAs and we demonstrate a role for lncRNAs in the regulation of transcriptional bursting of mRNAs.

scholarly journals Longitudinal monitoring of individual infection progression in Drosophila melanogaster

2021 ◽  
Author(s):  
Bryan A. Ramirez-Corona ◽  
Anna C. Love ◽  
Srikiran Chandrasekaran ◽  
Jennifer A. Prescher ◽  
Zeba Wunderlich
Keyword(s):  
Drosophila Melanogaster ◽  
Time Scale ◽  
Photon Flux ◽  
High Temporal Resolution ◽  
Non Invasive ◽  
Pathogen Load ◽  
The Hours ◽  
Imaging Strategy ◽  
Over Time ◽  
Stochastic Responses

The innate immune system is critical for host survival of infection. Infection models in organisms like Drosophila melanogaster are key for understanding evolution and dynamics of innate immunity. However, current toolsets for fly infection studies are limited in their ability to resolve changes in pathogen load on the hours time-scale, along with stochastic responses to infection in individuals. Here we report a novel bioluminescent imaging strategy enabling non-invasive characterization of pathogen load over time. We demonstrate that photon flux from autobioluminescent reporter bacteria can be used to estimate pathogen count. Escherichia coli expressing the ilux operon were imaged in whole, living flies at relevant concentrations for immune study. Because animal sacrifice was not necessary to estimate pathogen load, stochastic responses to infection were characterized in individuals for the first time. The high temporal resolution of bioluminescence imaging also enabled visualization of the fine dynamics of microbial clearance on the hours time-scale. Overall, this non-invasive imaging strategy provides a simple and scalable platform to observe changes in pathogen load in vivo over time.

scholarly journals Mutational Analysis of a Histone Deacetylase in Drosophila melanogaster: Missense Mutations Suppress Gene Silencing Associated With Position Effect Variegation

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 657-668 ◽  
Author(s):  
Randy Mottus ◽  
Richard E Sobel ◽  
Thomas A Grigliatti
Keyword(s):  
Drosophila Melanogaster ◽  
Histone Deacetylase ◽  
Transcriptional Activity ◽  
Mutational Analysis ◽  
Position Effect ◽  
Transcriptional Regulator ◽  
Position Effect Variegation ◽  
Missense Mutations ◽  
Effect Variegation ◽  
New Mutations

Abstract For many years it has been noted that there is a correlation between acetylation of histones and an increase in transcriptional activity. One prediction, based on this correlation, is that hypomorphic or null mutations in histone deacetylase genes should lead to increased levels of histone acetylation and result in increased levels of transcription. It was therefore surprising when it was reported, in both yeast and fruit flies, that mutations that reduced or eliminated a histone deacetylase resulted in transcriptional silencing of genes subject to telomeric and heterochromatic position effect variegation (PEV). Here we report the first mutational analysis of a histone deacetylase in a multicellular eukaryote by examining six new mutations in HDAC1 of Drosophila melanogaster. We observed a suite of phenotypes accompanying the mutations consistent with the notion that HDAC1 acts as a global transcriptional regulator. However, in contrast to recent findings, here we report that specific missense mutations in the structural gene of HDAC1 suppress the silencing of genes subject to PEV. We propose that the missense mutations reported here are acting as antimorphic mutations that “poison” the deacetylase complex and propose a model that accounts for the various phenotypes associated with lesions in the deacetylase locus.

scholarly journals Comparative approaches to the study of physiology: Drosophila as a physiological tool

2013 ◽  
Vol 304 (3) ◽  
pp. R177-R188 ◽  
Author(s):  
Wendi S. Neckameyer ◽  
Kathryn J. Argue
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Pattern Formation ◽  
Signaling Pathways ◽  
Human Disease ◽  
Cognitive Disorders ◽  
Model System ◽  
Critical Questions ◽  
Developmental Signaling ◽  
Shed Light

Numerous studies have detailed the extensive conservation of developmental signaling pathways between the model system, Drosophila melanogaster, and mammalian models, but researchers have also profited from the unique and highly tractable genetic tools available in this system to address critical questions in physiology. In this review, we have described contributions that Drosophila researchers have made to mathematical dynamics of pattern formation, cardiac pathologies, the way in which pain circuits are integrated to elicit responses from sensation, as well as the ways in which gene expression can modulate diverse behaviors and shed light on human cognitive disorders. The broad and diverse array of contributions from Drosophila underscore its translational relevance to modeling human disease.

Structure of the insect head as revealed by the EN protein pattern in developing embryos

Development ◽  
1996 ◽  
Vol 122 (11) ◽  
pp. 3419-3432 ◽  
Author(s):  
B.T. Rogers ◽  
T.C. Kaufman
Keyword(s):  
Drosophila Melanogaster ◽  
Pattern Formation ◽  
Protein Pattern ◽  
Related Protein ◽  
Specific Expression ◽  
Tissue Specific Expression ◽  
Single Segment ◽  
Dorsal Ridge ◽  
Insect Embryos ◽  
Comparative Embryology

The structure of the insect head has long been a topic of enjoyable yet endless debate among entomologists. More recently geneticists and molecular biologists trying to better understand the structure of the head of the Dipteran Drosophila melanogaster have joined the discourse extrapolating from what they have learned about Drosophila to insects in general. Here we present the results of an investigation into the structure of the insect head as revealed by the distribution of engrailed related protein (Engrailed) in the insect orders Diptera, Siphonaptera, Orthoptera and Hemiptera. The results of this comparative embryology in conjunction with genetic experiments on Drosophila melanogaster lead us to conclude: (1) The insect head is composed of six Engrailed accumulating segments, four postoral and two preoral. The potential seventh and eighth segments (clypeus or labrum) do not accumulate Engrailed. (2) The structure known as the dorsal ridge is not specific to the Diptera but is homologous to structures found in other insect orders. (3) A part of this structure is a single segment-like entity composed of labial and maxillary segment derivatives which produce the most anterior cuticle capable of taking a dorsal fate. The segments anterior to the maxillary segment produce only ventral structures. (4) As in Drosophila, the process of segmentation of the insect head is fundamentally different from the process of segmentation in the trunk. (5) The pattern of Engrailed accumulation and its presumed role in the specification and development of head segments appears to be highly conserved while its role in other pattern formation events and tissue-specific expression is variable. An overview of the pattern of Engrailed accumulation in developing insect embryos provides a basis for discussion of the generality of the parasegment and the evolution of Engrailed patterns.

scholarly journals Selection on wing allometry in Drosophila melanogaster.

Genetics ◽  
1990 ◽  
Vol 126 (4) ◽  
pp. 975-989 ◽  
Author(s):  
K E Weber
Keyword(s):  
Drosophila Melanogaster ◽  
Additive Genetic Variance ◽  
Bivariate Distribution ◽  
Local Optimum ◽  
Phenotypic Variance ◽  
Isofemale Lines ◽  
Developmental Patterns ◽  
Environmental Regimes ◽  
The Mean ◽  
Lateral Offset

Abstract Five bivariate distributions of wing dimensions of Drosophila melanogaster were measured, in flies 1) subjected to four defined environmental regimes during development, 2) taken directly from nature in seven U.S. states, 3) selected in ten populations for change in wing form, and 4) sampled from 21 long inbred wild-type lines. Environmental stresses during development altered both wing size and the ratios of wing dimensions, but regardless of treatment all wing dimensions fell near a common allometric baseline in each bivariate distribution. The wings of wild-caught flies from seven widely separated localities, and of their laboratory-reared offspring, also fell along the same baselines. However, when flies were selected divergently for lateral offset from these developmental baselines, response to selection was rapid in every case. The mean divergence in offset between oppositely selected lines was 14.68 SD of the base population offset, after only 15 generations of selection at 20%. Measurements of 21 isofemale lines, founded from wild-caught flies and maintained in small populations for at least 22 years, showed large reductions in phenotypic variance of offsets within lines, but a large increase in the variance among lines. The variance of means of isofemale lines within collection localities was ten times the variance of means among localities of newly established wild lines. These observations show that much additive genetic variance exists for individual dimensions within the wing, such that bivariate developmental patterns can be changed in any direction by selection or by drift. The relative invariance of the allometric baselines of wing morphology in nature is most easily explained as the result of continuous natural selection around a local optimum of functional design.

scholarly journals Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels

2016 ◽  
Author(s):  
Roy D. Dar ◽  
Sydney M. Schaffer ◽  
Siddarth S. Dey ◽  
Jonathan E. Foley ◽  
Abhyudai Singh ◽  
...  
Keyword(s):  
Conflict Of Interest ◽  
Burst Size ◽  
Inverse Correlation ◽  
Recent Analysis ◽  
Mrna Levels ◽  
Burst Frequency ◽  
Expression Variability ◽  
Protein Levels ◽  
Transcriptional Bursting ◽  
Cell Expression

Recent analysis (Dey et al, 2015), demonstrates that the HIV-1 Long Terminal Repeat (HIV LTR) promoter exhibits a range of possible transcriptional burst sizes and frequencies for any mean-expression level. However, these results have also been interpreted as demonstrating that cell-to-cell expression variability (noise) and mean are uncorrelated, a significant deviation from previous results. Here, we re-examine the available mRNA and protein abundance data for the HIV LTR and find that noise in mRNA and protein expression scales inversely with the mean along analytically predicted transcriptional burst-size manifolds. We then experimentally perturb transcriptional activity to test a prediction of the multiple burst-size model: that increasing burst frequency will cause mRNA noise to decrease along given burst-size lines as mRNA levels increase. The data show that mRNA and protein noise decrease as mean expression increases, supporting the canonical inverse correlation between noise and mean.Conflict of InterestThe authors declare that they have no conflict of interest.

Stripes of positional homologies across the wing blade of Drosophila melanogaster

Development ◽  
1988 ◽  
Vol 103 (2) ◽  
pp. 391-401 ◽  
Author(s):  
P. Simpson ◽  
M. El Messal ◽  
J. Moscoso del Prado ◽  
P. Ripoll
Keyword(s):  
Drosophila Melanogaster ◽  
Pattern Formation ◽  
Epidermal Cell ◽  
Correct Decision ◽  
Dorsoventral Axis ◽  
Anteroposterior Axis ◽  
Different Types

Clones of cells mutant for shaggy transform all hairs into bristles on the wing blade of Drosophila. Different types of bristles are formed at different locations. It is shown that, although shaggy cells are unable to make a correct decision between an epidermal cell pathway and that of a sensory bristle, they are nevertheless able to respond correctly to positional cues. A compilation of many clones led to the construction of a map of positional homologies in which all of the cells in any one area will produce the same kind of bristle. The result is a series of stripes oriented perpendicular to the anteroposterior axis of the wing and parallel to the dorsoventral axis. The significance of these stripes in relation to mechanisms of pattern formation is discussed.

Effects of respiratory afferent stimulation on phrenic neurogram during hypoxic gasping in the cat

1993 ◽  
Vol 75 (5) ◽  
pp. 2091-2098 ◽  
Author(s):  
J. E. Melton ◽  
L. O. Chae ◽  
N. H. Edelman
Keyword(s):  
Pattern Formation ◽  
Carotid Sinus ◽  
Superior Laryngeal Nerve ◽  
Laryngeal Nerve ◽  
Carotid Sinus Nerve ◽  
Burst Frequency ◽  
Burst Pattern ◽  
Progressive Hypoxia ◽  
Stimulation Period ◽  
Stimulation Of

Previous studies suggested that phrenic motor output is largely refractory to afferent stimuli during gasping. We tested this concept by electrically stimulating the carotid sinus nerve (CSN) or the superior laryngeal nerve (SLN) of anesthetized peripherally chemodenervated vagotomized ventilated cats during eupnea or gasping induced by hypoxia. During eupnea, phrenic neurogram amplitude (PNA) increased by 110% during 30 s of supramaximal CSN stimulation, but burst frequency did not change. Progressive hypoxia caused gasping after arterial O2 content was reduced by 75%. During gasping, CSN stimulation caused premature onset of gasp in 12 of 13 trials, shortened intergasp interval [6.3 +/- 0.9 vs. 14.8 +/- 2.5 (SE) s], and resulted in a small (20%) but significant increase in PNA. Intensity of SLN stimulation was adjusted to abolish phrenic activity during the 30-s eupneic stimulation period. During gasping, SLN stimulation of the same intensity tended to delay onset of the next gasp, increased intergasp interval (16.9 +/- 1.9 vs. 13.3 +/- 1.2 s), and reduced PNA by 32%. Thus the respiratory burst pattern formation circuitry responds to afferent stimuli during gasping, albeit in a manner different from the eupneic response. These observations suggest that gasping is the output of a modified eupneic burst pattern formation circuit.

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