MicroRNA (miRNA) are small, non-coding RNAs that affect gene expression through degradation of complementary mRNA targets or inhibition of translation. As they affect approximately 50% of all cellular processes, miRNA are tightly regulated by the cell through transcriptional and post-transcriptional mechanisms. Transcribed miRNA are capped and polyadenylated (referred to as pri-miRNA) which are cleaved by Drosha and DGCR8 to generate 60-90 nucleotide precursor miRNA. The precursors are cleaved again by Dicer and loaded into the RNA-induced silencing complex (RISC) of which Argonaute 2 is the functional component. Many of the proteins involved in miRNA biogenesis share a common role in ribosomal RNA regulation. Here we characterize two ribosome-associated proteins that are important for miRNA biogenesis. In one study, we identified nucleolin as a positive regulator of pri-miR-15a/miR-16-1 biogenesis. Nucleolin expression is inversely proportional to mature miR-15a/miR-16-1 expression. While nuclear localization of nucleolin increases miR-15a/16-1 expression, cytoplasmic localization of nucleolin decreases it in a mechanism dependent on the interaction of nucleolin with Drosha and DGCR8. Furthermore, pri-miR-15a/miR-16-1 is bound by nucleolin, which facilitates its processing in vitro. In another study, we analyzed TCGA patient datasets to uncover a miRNA signature associated with ZEB1/2 expression that refutes current models of miR-200 family (miR-200a/b/c, miR-141, miR-429) regulation. In breast cancer cell lines with low miR-200 expression an abundance of primary and precursor species exist. We found these precursors are able to regulate other miR-200 family members in a coherent feedforward loop, independent of transcription, by titrating away a repressor complex. We identified the repressor as Receptor of Ribosome Binding Protein 1 (RRBP1) by developing a new technique to capture endogenous protein-RNA complexes in vivo called Cross-linking and PNA Pulldown (CLaPP) assay. RRBP1 inversely correlates with miR-200 expression in cell lines and through gain- and loss-of-function studies. TGF-b treatment transcriptionally increased RRBP1 abundance resulting in loss of miR-200 expression. Lastly, RRBP1 was found to directly associate with miR-200 precursors through iCLIP analysis.
In summary, the ribosome-associated proteins nucleolin and RRBP1 were identified and characterized as two novel proteins involved in miRNA biogenesis, each forming feedforward miRNA loops that regulate distinct cellular processes.
","abstract_html":"<p>MicroRNA (miRNA) are small, non-coding RNAs that affect gene expression through degradation of complementary mRNA targets or inhibition of translation. As they affect approximately 50% of all cellular processes, miRNA are tightly regulated by the cell through transcriptional and post-transcriptional mechanisms. Transcribed miRNA are capped and polyadenylated (referred to as pri-miRNA) which are cleaved by Drosha and DGCR8 to generate 60-90 nucleotide precursor miRNA. The precursors are cleaved again by Dicer and loaded into the RNA-induced silencing complex (RISC) of which Argonaute 2 is the functional component. Many of the proteins involved in miRNA biogenesis share a common role in ribosomal RNA regulation. Here we characterize two ribosome-associated proteins that are important for miRNA biogenesis. In one study, we identified nucleolin as a positive regulator of pri-miR-15a/miR-16-1 biogenesis. Nucleolin expression is inversely proportional to mature miR-15a/miR-16-1 expression. While nuclear localization of nucleolin increases miR-15a/16-1 expression, cytoplasmic localization of nucleolin decreases it in a mechanism dependent on the interaction of nucleolin with Drosha and DGCR8. Furthermore, pri-miR-15a/miR-16-1 is bound by nucleolin, which facilitates its processing <em>in vitro</em>. In another study, we analyzed TCGA patient datasets to uncover a miRNA signature associated with ZEB1/2 expression that refutes current models of miR-200 family (miR-200a/b/c, miR-141, miR-429) regulation. In breast cancer cell lines with low miR-200 expression an abundance of primary and precursor species exist. We found these precursors are able to regulate other miR-200 family members in a coherent feedforward loop, independent of transcription, by titrating away a repressor complex. We identified the repressor as Receptor of Ribosome Binding Protein 1 (RRBP1) by developing a new technique to capture endogenous protein-RNA complexes <em>in vivo</em> called Cross-linking and PNA Pulldown (CLaPP) assay. RRBP1 inversely correlates with miR-200 expression in cell lines and through gain- and loss-of-function studies. TGF-b treatment transcriptionally increased RRBP1 abundance resulting in loss of miR-200 expression. Lastly, RRBP1 was found to directly associate with miR-200 precursors through iCLIP analysis.</p> <p>In summary, the ribosome-associated proteins nucleolin and RRBP1 were identified and characterized as two novel proteins involved in miRNA biogenesis, each forming feedforward miRNA loops that regulate distinct cellular processes.</p>","abstract_has_math":false,"creators":["Pickering, Brian"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation (PhD)","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Dihua Yu, MD, PhD","Ann-Bin Shyu, PhD","Dos Sarbassov, PhD"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-05-01T07:00:00Z","date_published":"2014-05-01T07:00:00Z","updated_at":"2026-07-24T05:50:31Z","subjects":["Nucleolin","RRBP1","p180","ES130","breast cancer","CLaPP","Cancer Biology","Medicine and Health Sciences","Molecular Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.library.tmc.edu/utgsbs_dissertations/460","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Dihua Yu, MD, PhD","Ann-Bin Shyu, PhD","Dos Sarbassov, PhD"]},{"key":"dc:creator","label":"Author","values":["Pickering, Brian"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2015-05-05T07:00:00Z"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation (PhD)"]},{"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":["Nucleolin","RRBP1","p180","ES130","breast cancer","CLaPP","Cancer Biology","Medicine and Health Sciences","Molecular Biology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.library.tmc.edu/utgsbs_dissertations/460"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["MicroRNA (miRNA) are small, non-coding RNAs that affect gene expression through degradation of complementary mRNA targets or inhibition of translation. As they affect approximately 50% of all cellular processes, miRNA are tightly regulated by the cell through transcriptional and post-transcriptional mechanisms. Transcribed miRNA are capped and polyadenylated (referred to as pri-miRNA) which are cleaved by Drosha and DGCR8 to generate 60-90 nucleotide precursor miRNA. The precursors are cleaved again by Dicer and loaded into the RNA-induced silencing complex (RISC) of which Argonaute 2 is the functional component. Many of the proteins involved in miRNA biogenesis share a common role in ribosomal RNA regulation. Here we characterize two ribosome-associated proteins that are important for miRNA biogenesis. In one study, we identified nucleolin as a positive regulator of pri-miR-15a/miR-16-1 biogenesis. Nucleolin expression is inversely proportional to mature miR-15a/miR-16-1 expression. While nuclear localization of nucleolin increases miR-15a/16-1 expression, cytoplasmic localization of nucleolin decreases it in a mechanism dependent on the interaction of nucleolin with Drosha and DGCR8. Furthermore, pri-miR-15a/miR-16-1 is bound by nucleolin, which facilitates its processing in vitro. In another study, we analyzed TCGA patient datasets to uncover a miRNA signature associated with ZEB1/2 expression that refutes current models of miR-200 family (miR-200a/b/c, miR-141, miR-429) regulation. In breast cancer cell lines with low miR-200 expression an abundance of primary and precursor species exist. We found these precursors are able to regulate other miR-200 family members in a coherent feedforward loop, independent of transcription, by titrating away a repressor complex. We identified the repressor as Receptor of Ribosome Binding Protein 1 (RRBP1) by developing a new technique to capture endogenous protein-RNA complexes in vivo called Cross-linking and PNA Pulldown (CLaPP) assay. RRBP1 inversely correlates with miR-200 expression in cell lines and through gain- and loss-of-function studies. TGF-b treatment transcriptionally increased RRBP1 abundance resulting in loss of miR-200 expression. Lastly, RRBP1 was found to directly associate with miR-200 precursors through iCLIP analysis.
In summary, the ribosome-associated proteins nucleolin and RRBP1 were identified and characterized as two novel proteins involved in miRNA biogenesis, each forming feedforward miRNA loops that regulate distinct cellular processes.
"]},{"key":"dc:title","label":"Title","values":["The Regulation of Microrna Biogenesis By Ribosome-Interacting Proteins"]}]}],"canonical_facts":{"dc:contributor":["Dihua Yu, MD, PhD","Ann-Bin Shyu, PhD","Dos Sarbassov, PhD"],"dc:creator":["Pickering, Brian"],"dc:date.available":["2015-05-05T07:00:00Z"],"dc:description.abstract":["MicroRNA (miRNA) are small, non-coding RNAs that affect gene expression through degradation of complementary mRNA targets or inhibition of translation. As they affect approximately 50% of all cellular processes, miRNA are tightly regulated by the cell through transcriptional and post-transcriptional mechanisms. Transcribed miRNA are capped and polyadenylated (referred to as pri-miRNA) which are cleaved by Drosha and DGCR8 to generate 60-90 nucleotide precursor miRNA. The precursors are cleaved again by Dicer and loaded into the RNA-induced silencing complex (RISC) of which Argonaute 2 is the functional component. Many of the proteins involved in miRNA biogenesis share a common role in ribosomal RNA regulation. Here we characterize two ribosome-associated proteins that are important for miRNA biogenesis. In one study, we identified nucleolin as a positive regulator of pri-miR-15a/miR-16-1 biogenesis. Nucleolin expression is inversely proportional to mature miR-15a/miR-16-1 expression. While nuclear localization of nucleolin increases miR-15a/16-1 expression, cytoplasmic localization of nucleolin decreases it in a mechanism dependent on the interaction of nucleolin with Drosha and DGCR8. Furthermore, pri-miR-15a/miR-16-1 is bound by nucleolin, which facilitates its processing in vitro. In another study, we analyzed TCGA patient datasets to uncover a miRNA signature associated with ZEB1/2 expression that refutes current models of miR-200 family (miR-200a/b/c, miR-141, miR-429) regulation. In breast cancer cell lines with low miR-200 expression an abundance of primary and precursor species exist. We found these precursors are able to regulate other miR-200 family members in a coherent feedforward loop, independent of transcription, by titrating away a repressor complex. We identified the repressor as Receptor of Ribosome Binding Protein 1 (RRBP1) by developing a new technique to capture endogenous protein-RNA complexes in vivo called Cross-linking and PNA Pulldown (CLaPP) assay. RRBP1 inversely correlates with miR-200 expression in cell lines and through gain- and loss-of-function studies. TGF-b treatment transcriptionally increased RRBP1 abundance resulting in loss of miR-200 expression. Lastly, RRBP1 was found to directly associate with miR-200 precursors through iCLIP analysis.
In summary, the ribosome-associated proteins nucleolin and RRBP1 were identified and characterized as two novel proteins involved in miRNA biogenesis, each forming feedforward miRNA loops that regulate distinct cellular processes.
"],"dc:identifier":["https://digitalcommons.library.tmc.edu/utgsbs_dissertations/460"],"dc:subject":["Nucleolin","RRBP1","p180","ES130","breast cancer","CLaPP","Cancer Biology","Medicine and Health Sciences","Molecular Biology"],"dc:title":["The Regulation of Microrna Biogenesis By Ribosome-Interacting Proteins"],"thesis:degree_level":["Dissertation (PhD)"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T05:50:31Z"}