scholarly journals Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

2019 ◽  
Author(s):  
Xuan G. Luong ◽  
Enrico Maria Daldello ◽  
Gabriel Rajkovic ◽  
Cai-Rong Yang ◽  
Marco Conti
Keyword(s):  
Mrna Translation ◽  
Messenger Rnas ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Meiotic Progression ◽  
Maternal Mrna ◽  
Highly Active ◽  
Genome Wide ◽  
Molecular Machinery ◽  
Maternal Mrnas

SummaryDuring oocyte maturation, changes in gene expression depend exclusively on translation and degradation of maternal mRNAs rather than transcription. Execution of this translation program is essential for assembling the molecular machinery required for meiotic progression, fertilization, and embryo development. With the present study, we used a RiboTag/RNA-Seq approach to explore the timing of maternal mRNA translation in quiescent oocytes as well as in oocytes progressing through the first meiotic division. This genome-wide analysis reveals a global switch in maternal mRNA translation coinciding with oocyte re-entry into the meiotic cell cycle. Messenger RNAs whose translation is highly active in quiescent oocytes invariably become repressed during meiotic re-entry, whereas transcripts repressed in quiescent oocytes become activated. Experimentally, we have defined the exact timing of the switch, the repressive function of CPE elements, and identified a novel role for CPEB1 in maintaining constitutive translation of a large group of maternal mRNAs during maturation.

scholarly journals Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

2020 ◽  
Vol 48 (6) ◽  
pp. 3257-3276 ◽  
Author(s):  
Xuan G Luong ◽  
Enrico Maria Daldello ◽  
Gabriel Rajkovic ◽  
Cai-Rong Yang ◽  
Marco Conti
Keyword(s):  
Mrna Translation ◽  
Messenger Rnas ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Meiotic Progression ◽  
Maternal Mrna ◽  
Highly Active ◽  
Genome Wide ◽  
Molecular Machinery ◽  
Maternal Mrnas

Abstract During oocyte maturation, changes in gene expression depend exclusively on translation and degradation of maternal mRNAs rather than transcription. Execution of this translation program is essential for assembling the molecular machinery required for meiotic progression, fertilization, and embryo development. With the present study, we used a RiboTag/RNA-Seq approach to explore the timing of maternal mRNA translation in quiescent oocytes as well as in oocytes progressing through the first meiotic division. This genome-wide analysis reveals a global switch in maternal mRNA translation coinciding with oocyte re-entry into the meiotic cell cycle. Messenger RNAs whose translation is highly active in quiescent oocytes invariably become repressed during meiotic re-entry, whereas transcripts repressed in quiescent oocytes become activated. Experimentally, we have defined the exact timing of the switch and the repressive function of CPE elements, and identified a novel role for CPEB1 in maintaining constitutive translation of a large group of maternal mRNAs during maturation.

Oocyte Maternal mRNA Translation and Developmental Competence: A Genome-Wide Analysis.

2012 ◽  
Vol 87 (Suppl_1) ◽  
pp. 88-88 ◽  
Author(s):  
Marco Conti ◽  
Jing Chen ◽  
Fang Xie ◽  
Chi-Jen Lin ◽  
Kathleen Horner
Keyword(s):  
Mrna Translation ◽  
Developmental Competence ◽  
Genome Wide Analysis ◽  
Maternal Mrna ◽  
Genome Wide ◽  
A Genome

scholarly journals An mRNA-binding channel in the ES6S region of the translation 48S-PIC promotes RNA unwinding and scanning

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Irene Díaz-López ◽  
René Toribio ◽  
Juan José Berlanga ◽  
Iván Ventoso
Keyword(s):  
Signal Transduction ◽  
Secondary Structure ◽  
Functional Model ◽  
Mrna Translation ◽  
Rna Helicases ◽  
Initiation Complex ◽  
Genome Wide Analysis ◽  
Scanning Process ◽  
Genome Wide ◽  
Mrna Binding

Loading of mRNA onto the ribosomal 43S pre-initiation complex (PIC) and its subsequent scanning require the removal of the secondary structure of the by RNA helicases such as eIF4A. However, the topology and mechanics of the scanning complex bound to mRNA (48S-PIC) and the influence of its solvent-side composition on the scanning process are poorly known. Here, we found that the ES6S region of the 48S-PIC constitutes an extended binding channel for eIF4A-mediated unwinding of mRNA and scanning. Blocking ES6S inhibited the cap-dependent translation of mRNAs that have structured 5′ UTRs (including G-quadruplexes), many of which are involved in signal transduction and growth, but it did not affect IRES-driven translation. Genome-wide analysis of mRNA translation revealed a great diversity in ES6S-mediated scanning dependency. Our data suggest that mRNA threading into the ES6S region makes scanning by 48S PIC slower but more processive. Hence, we propose a topological and functional model of the scanning 48S-PIC.

scholarly journals Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Maria Victoria Gomez Roldan ◽  
Farhaj Izhaq ◽  
Marion Verdenaud ◽  
John Eleblu ◽  
Aimen Haraghi ◽  
...  
Keyword(s):  
Gene Networks ◽  
Growth Arrest ◽  
Reproductive Organs ◽  
Stress Signaling ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Inhibition Of Growth ◽  
Genome Wide ◽  
Male Flowers

AbstractIn cucurbits, CmWIP1 is a master gene controlling sex determination. To bring new insight in the function of CmWIP1, we investigated two Arabidopsis WIP transcription factors, AtWIP1/TT1 and AtWIP2/NTT. Using an inducible system we showed that WIPs are powerful inhibitor of growth and inducer of cell death. Using ChIP-seq and RNA-seq we revealed that most of the up-regulated genes bound by WIPs display a W-box motif, associated with stress signaling. In contrast, the down-regulated genes contain a GAGA motif, a known target of polycomb repressive complex. To validate the role of WIP proteins in inhibition of growth, we expressed AtWIP1/TT1 in carpel primordia and obtained male flowers, mimicking CmWIP1 function in melon. Using other promoters, we further demonstrated that WIPs can trigger growth arrest of both vegetative and reproductive organs. Our data supports an evolutionary conserved role of WIPs in recruiting gene networks controlling growth and adaptation to stress.

Mutations that perturb poly(A)-dependent maternal mRNA activation block the initiation of development

Development ◽  
1996 ◽  
Vol 122 (2) ◽  
pp. 579-588 ◽  
Author(s):  
M.E. Lieberfarb ◽  
T. Chu ◽  
C. Wreden ◽  
W. Theurkauf ◽  
J.P. Gergen ◽  
...  
Keyword(s):  
Mrna Translation ◽  
Vital Role ◽  
Wild Type ◽  
Regulatory Pathway ◽  
Cytoplasmic Polyadenylation ◽  
Maternal Mrna ◽  
Independent Mechanism ◽  
Maternal Mrnas ◽  
Early Metazoan

Translational recruitment of maternal mRNAs is an essential process in early metazoan development. To identify genes required for this regulatory pathway, we have examined a collection of Drosophila female-sterile mutants for defects in translation of maternal mRNAs. This strategy has revealed that maternal-effect mutations in the cortex and grauzone genes impair translational activation and cytoplasmic polyadenylation of bicoid and Toll mRNAs. Cortex embryos contain a bicoid mRNA indistinguishable in amount, localization, and structure from that in wild-type embryos. However, the bicoid mRNA in cortex embryos contains a shorter than normal polyadenosine (poly(A)) tail. Injection of polyadenylated bicoid mRNA into cortex embryos allows translation demonstrating that insufficient polyadenylation prevents endogenous bicoid mRNA translation. In contrast nanos mRNA, which is activated by a poly(A)-independent mechanism, is translated in cortex embryos, indicating that the block in maternal mRNA activation is specific to a class of mRNAs. Cortex embryos are fertilized, but arrest at the onset of embryogenesis. Characterization of grauzone mutations indicates that the phenotype of these embryos is similar to cortex. These results identify a fundamental pathway that serves a vital role in the initiation of development.

scholarly journals Transposable element landscape in Drosophila populations selected for longevity

2019 ◽  
Author(s):  
Daniel K. Fabian ◽  
Handan Melike Dönertaş ◽  
Matías Fuentealba ◽  
Linda Partridge ◽  
Janet M. Thornton
Keyword(s):  
Drosophila Melanogaster ◽  
Telomere Maintenance ◽  
Rna Seq ◽  
Limited Evidence ◽  
Negative Effects ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Age Dependent ◽  
Genomic Insertions

ABSTRACTTransposable elements (TEs) inflict numerous negative effects on health and fitness as they replicate by integrating into new regions of the host genome. Even though organisms employ powerful mechanisms to demobilize TEs, transposons gradually lose repression during aging. The rising TE activity causes genomic instability and was implicated in age-dependent neurodegenerative diseases, inflammation and the determination of lifespan. It is therefore conceivable that long-lived individuals have improved TE silencing mechanisms resulting in reduced TE expression relative to their shorter-lived counterparts and fewer genomic insertions. Here, we test this hypothesis by performing the first genome-wide analysis of TE insertions and expression in populations of Drosophila melanogaster selected for longevity through late-life reproduction for 50-170 generations from four independent studies. Contrary to our expectation, TE families were generally more abundant in long-lived populations compared to non-selected controls. Although simulations showed that this was not expected under neutrality, we found little evidence for selection driving TE abundance differences. Additional RNA-seq analysis revealed a tendency for reducing TE expression in selected populations, which might be more important for lifespan than regulating genomic insertions. We further find limited evidence of parallel selection on genes related to TE regulation and transposition. However, telomeric TEs were genomically and transcriptionally more abundant in long-lived flies, suggesting improved telomere maintenance as a promising TE-mediated mechanism for prolonging lifespan. Our results provide a novel viewpoint indicating that reproduction at old age increases the opportunity of TEs to be passed on to the next generation with little impact on longevity.

scholarly journals Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection

2020 ◽  
Author(s):  
Tatiana V. Tkatchenko ◽  
Andrei V. Tkatchenko
Keyword(s):  
Circadian Clock ◽  
Eye Development ◽  
Genetic Network ◽  
Genetic Networks ◽  
Molecular Signaling ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Contrast Perception ◽  
Optical Defocus

SUMMARYRefractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. Here, we used genome-wide RNA-sequencing (RNA-seq) to conduct analysis of the retinal genetic networks underlying contrast perception and refractive eye development. We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.

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