Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
Results
Showing 1 to 20 of 41 for “"Ribosome profiling"”.
-
Translation-Mediated Stress Responses: Mining of Ribosome Profiling Data
… cellular mRNA fragments protected by translating ribosomes, dubbed ribosome profiling. This approach allows detection of differential translation activity, annotation of novel protein coding sequences and variants, identification of ribosome pause sites and estimates of de novo protein synthesis. …
-
A study of mRNA translation with computational analysis of ribosome profiling datasets
Ribosome profiling is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a “snapshot” of ribosome positions at the transcriptome wide level. The approach was developed in 2009 and was a significant advancement towards the better …
-
A study of mammalian microRNA-mediated repression of gene expression by ribosome profiling
… genome-wide scale. To address this gap, we used ribosome profiling to measure effects on protein production and compared these to simultaneously measured effects on mRNA levels. The latter were also quantified by a deep-sequencing approach (mRNA-Seq). This enabled us to obtain a snapshot of …
-
Development of a ribosome profiling protocol to study translation in the yeast Kluyveromyces marxianus
During mRNA translation, the ribosome protects ~28 nt of mRNA within its mRNA tunnel. Ribosome profiling is a method which takes advantage of this protected mRNA fragment, commonly referred to as the ribosome protected fragment (RPF). This method uses endonucleases to digest unprotected mRNA, …
-
The development of a ribosome profiling protocol to study translation in the yeast Yarrowia lipolytica
Ribosome Profiling is an emerging technique that provides a genome wide-view of translation in-vivo, allowing an in-depth analysis of translation within a cell. It offers significant advantages over other techniques such as RNA-sequencing for interpreting transcriptional data about cells. Ribosome …
-
Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation
Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon …
-
Representing translation: concepts, methods, and resources for protein coding loci representation and ribosome profiling data analysis
The advent of the ribosome profiling (Ribo-Seq) sequencing technique has led to the genome-wide characterisation of translatomic complexity across the tree of life. The understanding of the extent to which translation occurs outside of annotated protein coding regions has been greatly expanded, as …
-
Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression
… the viral translatome was characterised using ribosome profiling (RiboSeq), a high-throughput sequencing-based technique that allows the positions of translating ribosomes to be mapped to a genome with sub-codon precision. This was used in parallel with RNA sequencing (RNASeq) to analyse …
-
RNA G-quadruplexes and polyamines effects on translation: data analysis and development of software for ribosome pause prediction
Ribosome profiling (Ribo-seq) technique provides a global snapshot of actively translating ribosomes by capturing the ribosome protected mRNA fragments. Ribo-seq technique can be implemented to study various translation aspects such as differential gene expression at the translation level, …
-
Analysis of the Role of EIF5A in Mammalian Translation
… factor that has been demonstrated to relieve ribosome pauses during translation elongation at 'difficult to translate' peptide sequences in yeast and bacteria. We observed that eIF5A regulates protein isoform distribution of MYC, and that loss of function of this gene results in enhanced …
-
Translational mechanisms of stem cell fate regulation in epidermal oncogene tolerance
… but controlled growth. Using in vivo ribosome profiling, we reveal that eIF2B5 selectively regulates the translation of a substantial subset of the oncogenic RAS translatome. Furthermore, by coupling ribosome profiling with genetic screening, we provide direct functional evidence that …
-
Interrogating annotated protein coding regions for hitherto undetected translation
Ribosome profiling (Ribo-seq) is a technique that allows to capture ribosome protected fragments and sequence them. This powerful method enables discovery of not yet annotated proteoforms and translated open reading frames (ORFs), even ones that are hidden in annotated protein coding regions. Here …
-
RNA regulatory elements and translational control
… *Listeria monocytogenes* was analysed using a ribosome profiling method adapted for examination of bacteria which yielded single-nucleotide-resolution data. The ribosome profiles in combination with parallel RNA-Seq data were used to examine genetic elements that control translation, and were …
-
INVESTIGATING THE ROLE OF SPECIALIZED RIBOSOME DURING ERYTHROPOIESIS
Eukaryotic ribosomes are made up of ~80 ribosomal proteins (RPs) and 4 ribosomal RNAs (rRNAs), and are traditionally thought to be invariant in all cells. Recent studies have found that ribosomes can be heterogeneous in different cell types, and can regulate translation of specific subsets of …
-
Activity Based Profiling: New Insights into Metabolic Homeostasis
… the central nervous system using phosphorylated ribosome profiling. I will use this method to identify new neuronal populations that regulate energy balance as well as uncover new functions for well-studied neural populations. I will elaborate on key findings such as the role of prodynorphin, …
-
A multi-level approach of gene expression data analysis to investigate translatome dynamics across multiple tissues, stages, and mouse models of SMA
… SMN protein has been confirmed to be a ribosome-associated protein in vitro, in mouse cell lines and in vivo, and to physiologically regulate the translation of a particular subset of transcripts (defined as SMN-specific transcripts), which are characterized by specific sequence …
-
Expanding the applications of high-throughput DNA sequencing
… relevant fragments of DNA from cells. Ribosome profiling is an experimental technique that consists of sequencing short stretches of messenger RNAs that are protected from nuclease digestion by the presence of a bound ribosome. The resulting data represents millions of snapshots of the …
-
Translational defects in multiple tissues from the Smn2B/- mouse model of SMA.
… cutting-edge and sequencing-based techniques (ribosome profiling and RNA-seq) coupled with biochemical and molecular biology-based assay (polysome profiling, co-sedimentation profiles, qPCR, and western blotting), which applied to study in molecular detail the translational defects in the …
-
Comparative analysis of African and Asian/American Zika virus strains at the transcriptional and translational level
… at different levels. Firstly, RNA-Seq and ribosome profiling (Ribo-Seq) was performed on astrocytoma-glioblastoma cells (U251 cells) infected with an African and an American ZIKV strain to determine the transcriptional and translational profile of each virus. Two previously overlooked …
-
Ribosomal Proteins RPLP1 and RPLP2 are Host Factors Critically Required for Flavivirus Infectivity by Promoting Efficient Viral Translation Elongation.
… expressed DENV structural proteins. The ribosome profiling technique allowed us to quantitative map ribosomes across the transcriptome during early DENV infection in human cell lines depleted for RPLP1/2. We observed that local ribosome occupancy is altered in the viral open reading frame …
Page 1 of 3