The isomerization of uridine to pseudouridine (Ψ), known as pseudouridylation, is the most abundant post-transcriptional modification of stable RNAs. Due to technical limitations in pseudouridine detection methods, studies on pseudouridylation have historically focused on ribosomal RNAs, transfer RNAs, and spliceosomal small nuclear RNAs, where Ψs play a critical role in RNA biogenesis and function. For decades, Ψ research was confined to this small subset of cellular RNAs, owing to limitations in methods for Ψ detection. Interest in this modification was reinvigorated, however, with reports that Ψ is conditionally induced in different environmental contexts and that pseudouridylation of certain codons recoded amino acid incorporation. Pseudouridine has thus revealed itself as a dynamic modification capable of fine-tuning RNA function. In this thesis, I describe how I attempted to develop a high-throughput technique to identify novel sites of pseudouridylation throughout the whole transcriptome. By identifying what transcripts are subject to pseudouridylation, I hoped to better understand Ψ's functional role. While pursuing this work, a series of deep sequencing methods — Pseudo-seq, Ψ-seq, PSI-seq, and CeU-seq — were published that mapped Ψ positions across the entire transcriptome with single nucleotide resolution. Collectively, these methods greatly expanded the catalogue of pseudouridylated transcripts and revealed conditionally-dependent sites of pseudouridylation in response to cellular stress. With four techniques available, I undertook a critical analysis of their results, uncovering a comparatively small subset of robustly detectible putative Ψ sites. This analysis underscored the merits and limitations of each approach. Having identified areas for improvement in the available Ψ-detection approaches, I adapted Ψ-seq to profile sites of pseudouridylation in the protozoan parasite Trypanosoma brucei. My efforts at transcriptome-wide Ψ-detection, however, were undercut by an inability to experimentally replicate Ψ-seq. As much as this thesis documents an endeavor to better understand the functional role of pseudouridylation, it also documents systematic and thorough experimental failure. In so doing, the work detailed in this thesis highlights a need within the sciences to foster increased transparency and reproducibility.
","abstract_html":"<p>The isomerization of uridine to pseudouridine (Ψ), known as pseudouridylation, is the most abundant post-transcriptional modification of stable RNAs. Due to technical limitations in pseudouridine detection methods, studies on pseudouridylation have historically focused on ribosomal RNAs, transfer RNAs, and spliceosomal small nuclear RNAs, where Ψs play a critical role in RNA biogenesis and function. For decades, Ψ research was confined to this small subset of cellular RNAs, owing to limitations in methods for Ψ detection. Interest in this modification was reinvigorated, however, with reports that Ψ is conditionally induced in different environmental contexts and that pseudouridylation of certain codons recoded amino acid incorporation. Pseudouridine has thus revealed itself as a dynamic modification capable of fine-tuning RNA function. In this thesis, I describe how I attempted to develop a high-throughput technique to identify novel sites of pseudouridylation throughout the whole transcriptome. By identifying what transcripts are subject to pseudouridylation, I hoped to better understand Ψ's functional role. While pursuing this work, a series of deep sequencing methods — Pseudo-seq, Ψ-seq, PSI-seq, and CeU-seq — were published that mapped Ψ positions across the entire transcriptome with single nucleotide resolution. Collectively, these methods greatly expanded the catalogue of pseudouridylated transcripts and revealed conditionally-dependent sites of pseudouridylation in response to cellular stress. With four techniques available, I undertook a critical analysis of their results, uncovering a comparatively small subset of robustly detectible putative Ψ sites. This analysis underscored the merits and limitations of each approach. Having identified areas for improvement in the available Ψ-detection approaches, I adapted Ψ-seq to profile sites of pseudouridylation in the protozoan parasite Trypanosoma brucei. My efforts at transcriptome-wide Ψ-detection, however, were undercut by an inability to experimentally replicate Ψ-seq. As much as this thesis documents an endeavor to better understand the functional role of pseudouridylation, it also documents systematic and thorough experimental failure. In so doing, the work detailed in this thesis highlights a need within the sciences to foster increased transparency and reproducibility.</p>","abstract_has_math":false,"creators":["Zaringhalam, Maryam"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Nina Papavasiliou"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017-01-01T08:00:00Z","date_published":"2017-01-01T08:00:00Z","updated_at":"2026-07-24T04:11:45Z","subjects":["pseudouridylation","pseudouridine detection","Psi-seq","transcriptome mapping","Trypanosoma brucei","reproducibility","Life Sciences"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/391","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Nina Papavasiliou"]},{"key":"dc:creator","label":"Author","values":["Zaringhalam, Maryam"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["pseudouridylation","pseudouridine detection","Psi-seq","transcriptome mapping","Trypanosoma brucei","reproducibility","Life Sciences"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/391"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The isomerization of uridine to pseudouridine (Ψ), known as pseudouridylation, is the most abundant post-transcriptional modification of stable RNAs. Due to technical limitations in pseudouridine detection methods, studies on pseudouridylation have historically focused on ribosomal RNAs, transfer RNAs, and spliceosomal small nuclear RNAs, where Ψs play a critical role in RNA biogenesis and function. For decades, Ψ research was confined to this small subset of cellular RNAs, owing to limitations in methods for Ψ detection. Interest in this modification was reinvigorated, however, with reports that Ψ is conditionally induced in different environmental contexts and that pseudouridylation of certain codons recoded amino acid incorporation. Pseudouridine has thus revealed itself as a dynamic modification capable of fine-tuning RNA function. In this thesis, I describe how I attempted to develop a high-throughput technique to identify novel sites of pseudouridylation throughout the whole transcriptome. By identifying what transcripts are subject to pseudouridylation, I hoped to better understand Ψ's functional role. While pursuing this work, a series of deep sequencing methods — Pseudo-seq, Ψ-seq, PSI-seq, and CeU-seq — were published that mapped Ψ positions across the entire transcriptome with single nucleotide resolution. Collectively, these methods greatly expanded the catalogue of pseudouridylated transcripts and revealed conditionally-dependent sites of pseudouridylation in response to cellular stress. With four techniques available, I undertook a critical analysis of their results, uncovering a comparatively small subset of robustly detectible putative Ψ sites. This analysis underscored the merits and limitations of each approach. Having identified areas for improvement in the available Ψ-detection approaches, I adapted Ψ-seq to profile sites of pseudouridylation in the protozoan parasite Trypanosoma brucei. My efforts at transcriptome-wide Ψ-detection, however, were undercut by an inability to experimentally replicate Ψ-seq. As much as this thesis documents an endeavor to better understand the functional role of pseudouridylation, it also documents systematic and thorough experimental failure. In so doing, the work detailed in this thesis highlights a need within the sciences to foster increased transparency and reproducibility.
"]},{"key":"dc:title","label":"Title","values":["High Throughput Detection of Pseudouridine: Caveats, Conundrums, and a Case for Open Science"]}]}],"canonical_facts":{"dc:contributor":["Nina Papavasiliou"],"dc:creator":["Zaringhalam, Maryam"],"dc:description.abstract":["The isomerization of uridine to pseudouridine (Ψ), known as pseudouridylation, is the most abundant post-transcriptional modification of stable RNAs. Due to technical limitations in pseudouridine detection methods, studies on pseudouridylation have historically focused on ribosomal RNAs, transfer RNAs, and spliceosomal small nuclear RNAs, where Ψs play a critical role in RNA biogenesis and function. For decades, Ψ research was confined to this small subset of cellular RNAs, owing to limitations in methods for Ψ detection. Interest in this modification was reinvigorated, however, with reports that Ψ is conditionally induced in different environmental contexts and that pseudouridylation of certain codons recoded amino acid incorporation. Pseudouridine has thus revealed itself as a dynamic modification capable of fine-tuning RNA function. In this thesis, I describe how I attempted to develop a high-throughput technique to identify novel sites of pseudouridylation throughout the whole transcriptome. By identifying what transcripts are subject to pseudouridylation, I hoped to better understand Ψ's functional role. While pursuing this work, a series of deep sequencing methods — Pseudo-seq, Ψ-seq, PSI-seq, and CeU-seq — were published that mapped Ψ positions across the entire transcriptome with single nucleotide resolution. Collectively, these methods greatly expanded the catalogue of pseudouridylated transcripts and revealed conditionally-dependent sites of pseudouridylation in response to cellular stress. With four techniques available, I undertook a critical analysis of their results, uncovering a comparatively small subset of robustly detectible putative Ψ sites. This analysis underscored the merits and limitations of each approach. Having identified areas for improvement in the available Ψ-detection approaches, I adapted Ψ-seq to profile sites of pseudouridylation in the protozoan parasite Trypanosoma brucei. My efforts at transcriptome-wide Ψ-detection, however, were undercut by an inability to experimentally replicate Ψ-seq. As much as this thesis documents an endeavor to better understand the functional role of pseudouridylation, it also documents systematic and thorough experimental failure. In so doing, the work detailed in this thesis highlights a need within the sciences to foster increased transparency and reproducibility.
"],"dc:identifier":["https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/391"],"dc:subject":["pseudouridylation","pseudouridine detection","Psi-seq","transcriptome mapping","Trypanosoma brucei","reproducibility","Life Sciences"],"dc:title":["High Throughput Detection of Pseudouridine: Caveats, Conundrums, and a Case for Open Science"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T04:11:45Z"}