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.
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Showing 1 to 13 of 13 for “"Intron retention"”.
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Intron Retention Induced Neoantigen as Biomarkers in Diseases
… aberrant peptides derived from unspliced introns can be presented by the major histocompatibility complex (MHC) class I molecules on the cell surface and elicit immunogenicity. In this dissertation, we first developed an integrated computational pipeline for identifying IR-induced …
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Validating the WD Repeat Protein CDC40 as a Potential Therapeutic Target for Lung Cancer
… addition to a higher number of transcripts with intron retention. I explored one specific intron retention event in the mRNA transcript of the cell cycle regulatory protein CDCA5, a potential prognostic marker for cancer, and showed that CDC40 knockdown induced retention of its first intron …
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Ανάλυση των μοτίβων ματίσματος σε γονίδια που εμπλέκονται στην πρώιμη εκδήλωση Συστηματικού Ερυθηματώδους Λύκου
… εξονίων (exon skipping), συγκράτηση ιντρονίων (intron retention) και εναλλακτικά σημεία δότη-λήπτη (alternative donor and acceptor sites). Βιβλιογραφικά δεδομένα υποδηλώνουν ότι η συγκράτηση ιντρονίων μπορεί να λειτουργεί ως ρυθμιστικός μηχανισμός που οδηγεί σε καθυστερημένη γονιδιακή έκφραση, …
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BIOINFORMATICS ANALYSIS OF FULL-LENGTH RNA NANOPORE SEQUENCING AT SINGLE CELL LEVEL TO STUDY TRANSCRIPTIONAL AND MUTATIONAL PATTERNS IN HUMAN LEUKEMIA
… analyses revealed prevalent exon skipping and intron retention in AML samples. AML cells with the SRSF2 mutation exhibited significantly higher proportions of genes with multiple isoforms or novel transcripts. These findings illuminate the intricate connections between genetic complexity, …
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Integrative analysis of transcriptomic data to elucidate regulators of pre-mRNA processing
… MAJIQ’s superior accuracy and ability to handle intron retention enables more robust splicing quantification across tissues (GTEx) and improves the discovery of splicing QTLs (sQTLs), as demonstrated by validated MAJIQ-sQTLs in \textit{CYP11B1} (Chapter 3). Chapter 4 presents benchmarking work …
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Cytochrome P450 mRNA profile in human breast cancer cell lines.
… primer sets were used to demonstrate potential intron retention in CYP4Z1. Using established in vitro models for the study of regulatory mechanisms of CYP4Z1, T47D and ZR-75-1 BCCs were used in order to determine the appropriate nuclear receptors - i.e. progesterone receptor, glucocorticoid …
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Latency, Expression and Splicing During Infection With HIV
… primary cells. Infection with HIV89.6 increased intron retention in cellular genes and abundance of RNA from human endogenous retroviruses. We also quantified the frequency and location of chimeric HIV-host RNAs. These two studies together provided a detailed accounting of both HIV89.6 and host …
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Discovery and characterization of stable introns in yeast
Spliceosomal introns are a defining feature of eukaryotes; they are present in all known eukaryotic genomes, absent from all known non-eukaryotic genomes, and their accurate removal is essential for mRNA maturation. Although smaller ncRNAs can be processed from introns, the introns themselves are …
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Identification of novel branch points reveals insights into RNA processing
… number of novel BPs both in annotated introns and other genomic regions. We attempted to verify these novel introns using RNA-seq and Lariat-seq and surprisingly observed considerable amounts of alternative splicing (AS) in S. cerevisiae beyond the previously known stress-regulated …
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Isoform-Specific Expression During Embryo Development in Arabidopsis and Soybean
… several instances of exon skipping and intron retention as products of alternative splicing. The coding potential of the splice variants were evaluated using CodeWise. I developed CodeWise, a weighted support vector machine classifier to assess the coding potential of novel transcripts …
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Post-transcriptional regulation of poly(A) binding proteins direct multiple facets of cardiac development and hypertrophy
… that PABPN1 expression is controlled through intron retention and nuclear sequestration. Taken together, this dissertation presents a comprehensive model for the regulation of cardiac protein synthesis and hypertrophy in a physiologic context through multiple post-transcriptional mechanisms.
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The Placenta Methylome: Novel Insights into DNA Modifications in the Human Placenta
… all samples were found to be enriched within intronic regions and short tandem repeats ((CA)n, (GT)n, (CACACA)n). This work is the first to characterise non-CpG methylation in placentas and highlight potential novel epigenetic regulatory mechanisms. The CpG methylation profile in the placenta …
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Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data
… on the proteome. The results show that intron retention events lead to decreased protein abundance. It is also shown that differential transcript usage and gene expression have effects on protein abundance, altering it proportionally to transcript levels. Overall, some links between …