{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/125749"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/125749","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"RNA binding proteins and snoRNAs change the ribosome dynamics in translation","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","abstract_has_math":false,"creators":["Chowdhury, Mashiat Nawar"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biochemistry","degree_department":null,"school":null,"contributors":["Jin, Hong","Kalsotra, Auinash","Huang, Raven","Ceman, Stephanie"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-06-27","date_published":"2024-06-27","updated_at":"2026-07-22T22:25:02Z","subjects":["Rna","Rna Binding Proteins","Snorna","Translation"],"languages":["en","eng"],"rights":["Copyright 2024 Mashiat Nawar Chowdhury"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/125749","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Jin, Hong","Kalsotra, Auinash","Huang, Raven","Ceman, Stephanie"]},{"key":"dc:creator","label":"Author","values":["Chowdhury, Mashiat Nawar"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2024-06-27","2024-08"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biochemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Rna","Rna Binding Proteins","Snorna","Translation"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2024 Mashiat Nawar Chowdhury"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/125749"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","The student, Mashiat Nawar Chowdhury, accepted the attached license on 2024-06-06 at 14:32.","The student, Mashiat Nawar Chowdhury, submitted this Dissertation for approval on 2024-06-06 at 14:36.","This Dissertation was approved for publication on 2024-06-27 at 13:52.","DSpace SAF Submission Ingestion Package generated from Vireo submission #20824 on 2025-02-04 at 21:24:53","Translation regulation is an essential part of the control of gene expression. The unexpected gap between the expression of the genome at the level of transcriptome and proteome demonstrates pervasiveness and importance of translational regulation. One key feature of translation is that different mRNAs are translated at varying efficiencies. This results from differences in the molecular signature of the mRNA and translational machinery, and how they interact with each other. In general, regulation takes place at each step of the translation process including initiation, elongation, termination and recycling, during which, mRNA, their interacting protein partners, and the ribosome interact together to determine how an mRNA is translated. Proteins, such as RNA-binding proteins, often regulate translation at a gene specific level, changes in the ribosome often affect cellular mRNA translation at a global level. RGG domain containing proteins are evolutionary conserved RNA binding proteins that play critical roles in many cellular processes including translation. Owing to near ubiquitous yet specific interactions with both RNAs and proteins conferred by the RGG motif, deletion or overexpression of the RGG proteins, as well as altering their post translational modification states, often disrupt delicate balance of their complex interaction network, leading to either a loss of function or a toxic gain of function of the RGG-protein. Therefore, understanding molecular mechanism of function of RGG-proteins, their specific interaction and regulation will provide insights into how its mis-regulation implicates in diseases. Several key aspects of the molecular mechanism of RGG-proteins in the translation control were elucidated through the study of yeast RGG protein Sbp1 at both genomic and biochemical level. Our results show that Sbp1 binds to AU rich sequence of its target mRNAs in vivo and represses translation initiation in a transcript-dependent manner. Sbp1 often targets transcripts that are involved in translation, translation fidelity, and ribosome biogenesis. Furthermore, presence of Sbp1 causes ribosomes to pause at the elongation and initiate a ring-shaped polysome morphology. Along with RBPs, site-specific covalent modifications of rRNA have long been of great interest because of their abundance and their conservation. Variations of rRNA modification states including under-methylation and under-pseudouridylation were reported to impair translation, but mechanistic details accounting for this phenomenon are not fully understood. The rRNA segments in the inter-subunit bridges of the ribosome undergo a substantial number of modifications. Many of these bridge regions contact with tRNAs and translation factors bound to the ribosome, thereby affecting protein synthesis. Helix 69 (H69) and A-site finger (ASF) are two such intersubunit bridge structures present in the large subunit and forms bridge B1a and bridge B2a, respectively, that joins the 40S and 60S. Through genomic and biochemical studies, an altered translational efficiency by mutant ribosomes lacking modifications in these functionally important regions of the ribosome was observed. Translation initiation and termination were affected when ribosomes lack rRNA modifications in the A-site finger (ASF) region. Moreover, both cap-dependent and cap-independent translations were repressed by the loss of ASF rRNA modifications, but only cap-independent translations are repressed by the loss of H69 rRNA modifications. The results shed insights into the roles of rRNA modifications play in protein synthesis."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["RNA binding proteins and snoRNAs change the ribosome dynamics in translation"]}]}],"canonical_facts":{"dc:contributor":["Jin, Hong","Kalsotra, Auinash","Huang, Raven","Ceman, Stephanie"],"dc:creator":["Chowdhury, Mashiat Nawar"],"dc:date":["2024-06-27","2024-08"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","The student, Mashiat Nawar Chowdhury, accepted the attached license on 2024-06-06 at 14:32.","The student, Mashiat Nawar Chowdhury, submitted this Dissertation for approval on 2024-06-06 at 14:36.","This Dissertation was approved for publication on 2024-06-27 at 13:52.","DSpace SAF Submission Ingestion Package generated from Vireo submission #20824 on 2025-02-04 at 21:24:53","Translation regulation is an essential part of the control of gene expression. The unexpected gap between the expression of the genome at the level of transcriptome and proteome demonstrates pervasiveness and importance of translational regulation. One key feature of translation is that different mRNAs are translated at varying efficiencies. This results from differences in the molecular signature of the mRNA and translational machinery, and how they interact with each other. In general, regulation takes place at each step of the translation process including initiation, elongation, termination and recycling, during which, mRNA, their interacting protein partners, and the ribosome interact together to determine how an mRNA is translated. Proteins, such as RNA-binding proteins, often regulate translation at a gene specific level, changes in the ribosome often affect cellular mRNA translation at a global level. RGG domain containing proteins are evolutionary conserved RNA binding proteins that play critical roles in many cellular processes including translation. Owing to near ubiquitous yet specific interactions with both RNAs and proteins conferred by the RGG motif, deletion or overexpression of the RGG proteins, as well as altering their post translational modification states, often disrupt delicate balance of their complex interaction network, leading to either a loss of function or a toxic gain of function of the RGG-protein. Therefore, understanding molecular mechanism of function of RGG-proteins, their specific interaction and regulation will provide insights into how its mis-regulation implicates in diseases. Several key aspects of the molecular mechanism of RGG-proteins in the translation control were elucidated through the study of yeast RGG protein Sbp1 at both genomic and biochemical level. Our results show that Sbp1 binds to AU rich sequence of its target mRNAs in vivo and represses translation initiation in a transcript-dependent manner. Sbp1 often targets transcripts that are involved in translation, translation fidelity, and ribosome biogenesis. Furthermore, presence of Sbp1 causes ribosomes to pause at the elongation and initiate a ring-shaped polysome morphology. Along with RBPs, site-specific covalent modifications of rRNA have long been of great interest because of their abundance and their conservation. Variations of rRNA modification states including under-methylation and under-pseudouridylation were reported to impair translation, but mechanistic details accounting for this phenomenon are not fully understood. The rRNA segments in the inter-subunit bridges of the ribosome undergo a substantial number of modifications. Many of these bridge regions contact with tRNAs and translation factors bound to the ribosome, thereby affecting protein synthesis. Helix 69 (H69) and A-site finger (ASF) are two such intersubunit bridge structures present in the large subunit and forms bridge B1a and bridge B2a, respectively, that joins the 40S and 60S. Through genomic and biochemical studies, an altered translational efficiency by mutant ribosomes lacking modifications in these functionally important regions of the ribosome was observed. Translation initiation and termination were affected when ribosomes lack rRNA modifications in the A-site finger (ASF) region. Moreover, both cap-dependent and cap-independent translations were repressed by the loss of ASF rRNA modifications, but only cap-independent translations are repressed by the loss of H69 rRNA modifications. The results shed insights into the roles of rRNA modifications play in protein synthesis."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/125749"],"dc:language":["en","eng"],"dc:rights":["Copyright 2024 Mashiat Nawar Chowdhury"],"dc:subject":["Rna","Rna Binding Proteins","Snorna","Translation"],"dc:title":["RNA binding proteins and snoRNAs change the ribosome dynamics in translation"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Biochemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:02Z"}