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Author: Stephen William Eichhorn Publisher: ISBN: Category : Languages : en Pages : 286
Book Description
Eukaryotic mRNAs have a cap structure at their 5' ends and a poly(A) tail at their 3' ends, and the proteins that bind these features increase the stability and translation of an mRNA. The influence of the poly(A) tail on translation was discovered decades ago, but primarily with regard to the idea that an mRNA with a poly(A) tail is better translated than one without. The influence of differences in tail length on translation had been assessed for just a few mRNAs, and in these cases long-tailed mRNAs were better translated than short-tailed mRNAs. We measured the poly(A)-tail length and translational efficiency of mRNAs corresponding to thousands of different genes in 35 different cell types or contexts. Extending previous singlegene studies, we found a global relationship between tail length and translational efficiency in Drosophila oocytes, and Drosophila, Xenopus, and zebrafish embryos. Surprisingly, in all three species, the strong coupling between tail length and translational efficiency was lost once the embryos reached gastrulation, and there was no coupling in the post-embryonic contexts we examined. We thus demonstrated that poly(A)-tail length is a major determinant of translational efficiency during early animal development and discovered a broadly conserved developmental switch in translational control. During the tail-length regulatory regime of the early embryo, a protein or microRNA might regulate translation by changing the poly(A)-tail length of an mRNA, interacting with the translation machinery, or both mechanisms. We characterized the mechanism used by two translational regulatory proteins in Drosophila, finding that they predominantly act by regulating tail length. Likewise, in early zebrafish embryos, microRNAs repress the translation of their hundreds of mRNA targets by shortening poly(A) tails. Our findings indicate that much of the translational regulation in early development is achieved by regulating poly(A)-tail lengths. Outside of early embryonic contexts, microRNAs regulate gene expression by causing both translational repression and mRNA degradation. We greatly expanded the mammalian cell types and contexts in which the steady-state and pre-steady-state effects of a microRNA had been examined globally for endogenous mRNAs. In all post-embryonic contexts with substantial microRNA-mediated repression, the predominant mode of repression was mRNA degradation.
Author: Stephen William Eichhorn Publisher: ISBN: Category : Languages : en Pages : 286
Book Description
Eukaryotic mRNAs have a cap structure at their 5' ends and a poly(A) tail at their 3' ends, and the proteins that bind these features increase the stability and translation of an mRNA. The influence of the poly(A) tail on translation was discovered decades ago, but primarily with regard to the idea that an mRNA with a poly(A) tail is better translated than one without. The influence of differences in tail length on translation had been assessed for just a few mRNAs, and in these cases long-tailed mRNAs were better translated than short-tailed mRNAs. We measured the poly(A)-tail length and translational efficiency of mRNAs corresponding to thousands of different genes in 35 different cell types or contexts. Extending previous singlegene studies, we found a global relationship between tail length and translational efficiency in Drosophila oocytes, and Drosophila, Xenopus, and zebrafish embryos. Surprisingly, in all three species, the strong coupling between tail length and translational efficiency was lost once the embryos reached gastrulation, and there was no coupling in the post-embryonic contexts we examined. We thus demonstrated that poly(A)-tail length is a major determinant of translational efficiency during early animal development and discovered a broadly conserved developmental switch in translational control. During the tail-length regulatory regime of the early embryo, a protein or microRNA might regulate translation by changing the poly(A)-tail length of an mRNA, interacting with the translation machinery, or both mechanisms. We characterized the mechanism used by two translational regulatory proteins in Drosophila, finding that they predominantly act by regulating tail length. Likewise, in early zebrafish embryos, microRNAs repress the translation of their hundreds of mRNA targets by shortening poly(A) tails. Our findings indicate that much of the translational regulation in early development is achieved by regulating poly(A)-tail lengths. Outside of early embryonic contexts, microRNAs regulate gene expression by causing both translational repression and mRNA degradation. We greatly expanded the mammalian cell types and contexts in which the steady-state and pre-steady-state effects of a microRNA had been examined globally for endogenous mRNAs. In all post-embryonic contexts with substantial microRNA-mediated repression, the predominant mode of repression was mRNA degradation.
Author: Orna Resnekov Publisher: Springer Science & Business Media ISBN: 3642609295 Category : Science Languages : en Pages : 276
Book Description
Many important cellular processes rely on posttranscriptional control of gene expression. This book describes the mechanisms of gene expression at this level that occur in the cytoplasm of prokaryotes and eukaryotes. Several introductory chapters discuss the general principles of translation and mRNA stability. The interactions of mature mRNA with the translational machinery, the components of mRNA degradation and antisense RNA are surveyed. Subsequent chapters discuss protein folding, transport, modification and degradation. The book is an invaluable source of information for both newcomers and those wishing an overview of the field.
Author: Sarah Azoubel Lima Publisher: ISBN: Category : Languages : en Pages : 141
Book Description
Every step in the existence of a messenger mRNA is carefully regulated. I explored the impact of a feature present in the great majority of eukaryotic mRNAs: the poly(A) tail. Poly(A) tails are important elements in mRNA maturation, translation and stability, but only recently the tail lengths of mRNAs have been revealed on a transcriptome wide scale. I have adapted the poly(A) sequencing method TAIL-seq and developed aTAIL-seq (adapted TAIL-seq). Chapter 4 contains detailed protocols of aTAIL-seq and other methods of poly(A) analysis. In this work, I have applied aTAIL-seq to measure the poly(A) tails of Caenorhabditis elegans. The nematode C. elegans is an model organism that has been used to identify multiple conserved biological processes, including the discovery of microRNAs (reviewed in Chapter 2). In Chapter 3, I explore the relationship between the poly(A) tail, translation and stability in C. elegans and other eukaryotes. Traditionally, long tails have been thought to enhance translation and stability of mRNAs. However, we found that the most abundant types of mRNAs, such as those encoding ribosomal proteins, have the shortest tail lengths, while the least abundant, such as mRNAs for transcription factors, have the longest tails. This difference is related to translation efficiency, as genes enriched for optimal codons and ribosomal occupancy have the shortest median tails. These results suggest that translation promotes poly(A) tail shortening, an idea supported by our observation that non-coding RNAs carry long poly(A) tails. We find that, in general, the most abundant and well-translated mRNAs have the shortest median poly(A) tail lengths. While this study seems to contradict the dogma that deadenylation is associated with translational inhibition and mRNA decay, it actually points to a mechanism where well expressed mRNAs undergo pruning of their poly(A) tails to lengths that accommodate 1-2 poly(A) binding proteins (PABPs). This may be an optimal size for PABP to engage in protective and translational functions. Overall, our findings suggest that translation regulates pruning of poly(A) tails, either by actively promoting their shortening or by stabilizing the short-tailed mRNAs. This work changes our understanding of the regulation of poly(A) tail length and gene expression.
Author: Alexander Orest Subtelny Publisher: ISBN: Category : Languages : en Pages : 144
Book Description
Poly(A) tails are found at the 3' ends of nearly all eukaryotic messenger RNAs (mRNAs) and long non-coding RNAs. The presence of a poly(A) tail promotes translation and inhibits decay of an mRNA, with both effects mediated through poly(A)-binding protein. However, an understanding of the relationship between the length of a poly(A) tail and these aspects of mRNA metabolism has been limited, primarily because of the lack of a technology that provides high-resolution poly(A)-tail length measurements in a global manner. This dissertation describes a new, high-throughput-sequencing-based method (PAL-seq) that measures the tails of individual mRNA molecules by coupling a fluorescence-based readout of poly(A)-tail length with sequencing of the poly(A)-proximal region. Using PAL-seq, we have found that poly(A)-tail lengths exhibit a notably poor correlation with translational efficiency (as measured by ribosome profiling) across genes in nearly all systems we have examined. In contrast, early zebrafish and Xenopus laevis embryos display a striking correlation (Spearman R > 0.6) that disappears at gastrulation. This developmental uncoupling of tail length and translational efficiency explains the different outcomes of microRNA (miRNA)-mediated poly(A)-tail shortening in zebrafish embryos before and after gastrulation, with translational repression being the predominant effect before and mRNA destabilization after. We have also observed that poly(A)-tail lengths do not correlate positively with mRNA half-lives in mammalian cells, and that miRNAs do not promote any apparent tail shortening in this setting. Since these results could be explained by differences in deadenylation rates, we performed a kinetic analysis in which we captured newly-made mRNAs of different age ranges. The deadenylation rates that we calculated after measuring tails over time correlated strongly with mRNA half-lives (Spearman R
Author: Jacques Lapointe Publisher: Springer Science & Business Media ISBN: 9780306478390 Category : Science Languages : en Pages : 476
Book Description
Translation Mechanisms provides investigators and graduate students with overviews of recent developments in the field of protein biosynthesis that are fuelled by the explosive and synergic growth of structural biology, genomics, and bioinformatics. The outstanding progress in our understanding of the structure, dynamics, and evolution of the prokaryotic and eukaryotic translation machinery, as well as applications in medicine and biotechnology, are described in 26 chapters covering recent discoveries on: -the subtleties of tRNA aminoacylation with natural and unnatural amino acids. -the control of mRNA stability, a key step of gene regulation. -ribosome structure and function, in the era of the atomic-crystal resolution of the ribosome. -the regulation of the biosynthesis of the translational machinery components. -the action of a variety of inhibitors of translation and the prospect for clinical studies.
Author: Timothy Jonas Eisen Publisher: ISBN: Category : Languages : en Pages : 297
Book Description
Central to mRNA metabolism is the poly(A)-tail, a stretch of adenosine nucleotides at the mRNA 3' end. In this dissertation, I investigate the role of the tail in the dynamics of mRNA decay, and describe the predominant mechanisms of decay for thousands of mammalian mRNAs. Next, I examine the effects of microRNAs, which influence mRNA decay and perturb tail length dynamics. Finally, I describe a physiological context in which the tail helps to control translation: neurons of the mouse brain. mRNA decay is tightly regulated in eukaryotes, determining the steady-state abundances and rates of accumulation of mRNAs. Despite this central role, the dynamics of decay have been described for only a handful of mRNAs. We determine these dynamics for thousands of endogenous mRNAs. Nascent mRNAs have reproducible and heterogeneous tail lengths just after they escape the nucleus. Once in the cytoplasm, most mRNAs are substrates for deadenylation, the rates of which vary by over 1000-fold, a range sufficiently large to capture the variation in mRNA decay rates. Surprisingly, once their tails become short, mRNAs decay at rates that also span a 1000-fold range. Moreover, these rates are coupled to their deadenylation rates, suggesting a concerted process of remodeling the mRNA--protein complex during decay. MicroRNAs (miRNAs) are small RNAs that influence decay of mRNA targets by recruiting deadenylases. Despite this recruitment, we observe no changes to steady-state tail length for miRNA targets. Resolving this paradox, we find that miRNAs not only deadenylate their targets but also increase the decay rate of short-tailed target molecules. By enhancing both rates, miRNAs do not alter the distribution of tail lengths of target mRNAs but enhance the rate at which mRNAs traverse these lengths. Neurons have unique requirements for translational control. We perform ribosome profiling in primary neuronal cultures and brain tissues from a mouse. mRNA poly(A)-tail lengths explain some (~5%) of the large variance in translational efficiency we observe, as does coding-sequence length, expression level, and codon composition. For some mRNAs, neuronal stimulation modifies tail lengths, and for a subset, transcription cannot explain these changes. A linear model that uses known determinants to predict translational efficiency explains only a portion (30– 40%) of its variance, indicating the need for additional investigation of mechanisms of translation in neurons.
Author: Nahum Sonenberg Publisher: CSHL Press ISBN: 9780879696184 Category : Gene expression Languages : en Pages : 1034
Book Description
Since the 1996 publication of Translational Control, there has been fresh interest in protein synthesis and recognition of the key role of translation control mechanisms in regulating gene expression. This new monograph updates and expands the scope of the earlier book but it also takes a fresh look at the field. In a new format, the first eight chapters provide broad overviews, while each of the additional twenty-eight has a focus on a research topic of more specific interest. The result is a thoroughly up-to-date account of initiation, elongation, and termination of translation, control mechanisms in development in response to extracellular stimuli, and the effects on the translation machinery of virus infection and disease. This book is essential reading for students entering the field and an invaluable resource for investigators of gene expression and its control.
Author: Katherine Lee Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
The oocyte-to-embryo transition (OET) occurs in the absence of new transcription and relies on post-transcriptional gene regulation, including translational control by mRNA poly(A) tail regulation, where cytoplasmic polyadenylation activates translation and deadenylation leads to translational repression and decay. However, how the transcriptome-wide landscape of mRNA poly(A) tails shapes translation across the OET in mammals remains unknown. Here, we performed long-read RNA sequencing to uncover poly(A) tail lengths and mRNA abundance transcriptome-wide in mice across five stages of development from oocyte to embryo. Integrating these data with recently published ribosome profiling data, we demonstrate that poly(A) tail length is coupled to translational efficiency across the entire OET. We uncover an extended wave of global deadenylation during fertilization, which sets up a switch in translation control between the oocyte and embryo. In the oocyte, short-tailed maternal mRNAs that resist deadenylation in the oocyte are translationally activated, whereas large groups of mRNAs deadenylated without decay in the oocyte are later readenylated to drive translation activation in the early embryo. To investigate the mechanism, we have identified 3'UTR sequence motifs in activated and repressed transcripts and identified stage-specific candidates for RNA binding protein regulators. Our findings provide an important resource and insight into the mechanisms by which cytoplasmic polyadenylation and deadenylation dynamically shape poly(A) tail length in a stage-specific manner to orchestrate development from oocyte to embryo in mammals.
Author: Lucy W. Barrett Publisher: Springer Science & Business Media ISBN: 3034806795 Category : Science Languages : en Pages : 63
Book Description
There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as “junk DNA”, it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal and spatial gene expression through the combinatorial effect of numerous mechanisms and interactions working together to fine-tune gene expression. The major regions involved in regulation of a particular gene are the 5’ and 3’ untranslated regions and introns. In addition, pervasive transcription of complex genomes produces a variety of non-coding transcripts that interact with these regions and contribute to regulation. This book discusses recent insights into the regulatory roles of the untranslated gene regions and non-coding RNAs in the control of complex gene expression, as well as the implications of this in terms of organism complexity and evolution.
Author: Stephen William Eichhorn
Author: Stephen William Eichhorn
Author: Orna Resnekov
Author: Sarah Azoubel Lima
Author: Alexander Orest Subtelny
Author: Bruce Alberts
Author: Jacques Lapointe
Author: Timothy Jonas Eisen
Author: Nahum Sonenberg
Author: Katherine Lee
Author: Lucy W. Barrett