scholarly journals Application of Domain- and Genotype-Specific Models to Infer Post-Transcriptional Regulation of Segmentation Gene Expression in Drosophila

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1232
Author(s):  
Maria A. Duk ◽  
Vitaly V. Gursky ◽  
Maria G. Samsonova ◽  
Svetlana Yu. Surkova
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Protein Expression ◽  
Drosophila Embryo ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Wild Type ◽  
Segmentation Gene ◽  
Segmentation Gene Expression ◽  
Post Transcriptional Regulation

Unlike transcriptional regulation, the post-transcriptional mechanisms underlying zygotic segmentation gene expression in early Drosophila embryo have been insufficiently investigated. Condition-specific post-transcriptional regulation plays an important role in the development of many organisms. Our recent study revealed the domain- and genotype-specific differences between mRNA and the protein expression of Drosophila hb, gt, and eve genes in cleavage cycle 14A. Here, we use this dataset and the dynamic mathematical model to recapitulate protein expression from the corresponding mRNA patterns. The condition-specific nonuniformity in parameter values is further interpreted in terms of possible post-transcriptional modifications. For hb expression in wild-type embryos, our results predict the position-specific differences in protein production. The protein synthesis rate parameter is significantly higher in hb anterior domain compared to the posterior domain. The parameter sets describing Gt protein dynamics in wild-type embryos and Kr mutants are genotype-specific. The spatial discrepancy between gt mRNA and protein posterior expression in Kr mutants is well reproduced by the whole axis model, thus rejecting the involvement of post-transcriptional mechanisms. Our models fail to describe the full dynamics of eve expression, presumably due to its complex shape and the variable time delays between mRNA and protein patterns, which likely require a more complex model. Overall, our modeling approach enables the prediction of regulatory scenarios underlying the condition-specific differences between mRNA and protein expression in early embryo.

scholarly journals Natural Genetic Variation Modifies Gene Expression Dynamics at the Protein Level During Pheromone Response in Saccharomyces cerevisiae

2016 ◽  
Author(s):  
Daniel A. Pollard ◽  
Ciara K. Asamoto ◽  
Homa Rahnamoun ◽  
Austin S. Abendroth ◽  
Suzanne R. Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Genetic Variation ◽  
Steady State ◽  
Protein Expression ◽  
Expression Patterns ◽  
Synthesis Rate ◽  
Protein Synthesis Rate ◽  
Mrna Levels ◽  
Expression Divergence

ABSTRACTHeritable variation in gene expression patterns plays a fundamental role in trait variation and evolution, making understanding the mechanisms by which genetic variation acts on gene expression patterns a major goal for biology. Both theoretical and empirical work have largely focused on variation in steady-state mRNA levels and mRNA synthesis rates, particularly of protein-coding genes. Yet in order for this variation to affect higher order traits it must lead to differences at the protein level. Variation in protein-specific processes including protein synthesis rates and protein decay rates could amplify, mask, or even reverse effects transmitted from the transcript level, but the extent to which this happens is unclear. Moreover, mechanisms that underlie protein expression variation under dynamic conditions have not been examined. To address this challenge, we analyzed how mRNA and protein expression dynamics covary between two strains ofSaccharomyces cerevisiaeduring mating pheromone response. Although divergentsteady-statemRNA expression levels explained divergentsteady-stateprotein levels for four out of five genes in our study, the same was true for only one out of five genes for expressiondynamics. By integrating decay rate and allele-specific protein expression analyses, we resolved that expression divergence for Fig1p was caused by genetic variation acting intranson protein synthesis rate, expression divergence for Ina1p was caused bycis-by-transepistatic effects on transcript level and protein synthesis rate, and expression divergence for Fus3p and Tos6p were caused by divergence in protein synthesis rates. Our study demonstrates that steady-state analysis of gene expression is insufficient to understand the impact of genetic variation on gene expression variation. An integrated and dynamic approach to gene expression analysis - comparing mRNA levels, protein levels, protein decay rates, and allele-specific protein expression - allows for a detailed analysis of the genetic mechanisms underlying protein expression divergences.

fushi tarazu protein expression in the cellular blastoderm of Drosophila detected using a novel imaging technique

Development ◽  
1989 ◽  
Vol 106 (1) ◽  
pp. 95-103 ◽  
Author(s):  
T.L. Karr ◽  
T.B. Kornberg
Keyword(s):  
Transcriptional Regulation ◽  
Protein Expression ◽  
Transcriptional Control ◽  
Imaging Technique ◽  
Drosophila Embryo ◽  
Immunoperoxidase Technique ◽  
Fushi Tarazu ◽  
Post Transcriptional Regulation ◽  
Blastoderm Stage ◽  
Anterior Posterior

The fushi tarazu (ftz) gene is essential for segmentation of the Drosophila embryo. This requirement is reflected at the cellular blastoderm stage of embryogenesis by seven transverse stripes of ftz expression. These stripes correspond to the missing segments of ftz mutant embryos. We describe here novel intermediate patterns of ftz protein expression which were detected in younger embryos by using anti-ftz antibodies and a sensitive fluorescence/immunoperoxidase technique (‘filtered fluorescence imaging’, FFI). Striped patterns of ftz protein evolved continuously, and the different stripes appeared in an ordered sequence, involving both anterior-posterior (A/P) and dorsal-ventral (D/V) progressions. Comparison of these patterns of ftz protein with those of ftz RNA suggests that these novel aspects of the patterning process involve post-transcriptional regulation in addition to the transcriptional control known to be involved in expression of this gene.

scholarly journals Embryonic geometry underlies phenotypic variation in decanalized conditions

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Anqi Huang ◽  
Jean-François Rupprecht ◽  
Timothy E Saunders
Keyword(s):  
Gene Expression ◽  
Aspect Ratio ◽  
Phenotypic Variation ◽  
Drosophila Embryo ◽  
Wild Type ◽  
Gap Gene ◽  
Key Factor ◽  
Segmentation Gene Expression ◽  
Environmental Variations ◽  
Anterior Posterior

During development, many mutations cause increased variation in phenotypic outcomes, a phenomenon termed decanalization. Phenotypic discordance is often observed in the absence of genetic and environmental variations, but the mechanisms underlying such inter-individual phenotypic discordance remain elusive. Here, using the anterior-posterior (AP) patterning of the Drosophila embryo, we identified embryonic geometry as a key factor predetermining patterning outcomes under decanalizing mutations. With the wild-type AP patterning network, we found that AP patterning is robust to variations in embryonic geometry; segmentation gene expression remains reproducible even when the embryo aspect ratio is artificially reduced by more than twofold. In contrast, embryonic geometry is highly predictive of individual patterning defects under decanalized conditions of either increased bicoid (bcd) dosage or bcd knockout. We showed that the phenotypic discordance can be traced back to variations in the gap gene expression, which is rendered sensitive to the geometry of the embryo under mutations.

scholarly journals Fast and Efficient 5′P Degradome Library Preparation for Analysis of Co-Translational Decay in Arabidopsis

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 466
Author(s):  
Marie-Christine Carpentier ◽  
Cécile Bousquet-Antonelli ◽  
Rémy Merret
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Transcriptional Regulation ◽  
High Throughput ◽  
Library Preparation ◽  
Working Day ◽  
Set Up ◽  
Post Transcriptional Regulation ◽  
Commercial Kit

The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of a new decay pathway called co-translational mRNA decay. Thanks to these approaches, ribosome dynamics could now be revealed by analysis of 5′P reads accumulation. However, library preparation could be difficult to set-up for non-specialists. Here, we present a fast and efficient 5′P degradome library preparation for Arabidopsis samples. Our protocol was designed without commercial kit and gel purification and can be easily done in one working day. We demonstrated the robustness and the reproducibility of our protocol. Finally, we present the bioinformatic reads-outs necessary to assess library quality control.

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