{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/129913"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/129913","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Diverse primary and secondary structural features are associated with Y complex-dependent mRNA maturation in B. subtilis","abstract":"In Bacillus subtilis, mRNA processing and decay are primarily initiated by the endonuclease RNase Y. Recent work by our group discovered a set of auxiliary factors called the Y complex that is required for the mRNA maturation of 21 operons. It is unclear, however, how these operons specifically are targeted by RNase Y and the Y complex. Here we use in silico sequence motif searches, kmer analysis and secondary structure prediction to analyze these 21 cleavage sites and their surrounding regions. We find enrichment for a guanine immediately preceding the cleavage site. Such enrichment has been previously observed in Staphylococcus aureus RNase Y cleavage sites, indicating a role for the Y complex in processing those sites as well. Surprisingly, there are no other detectable sequence or structural motifs in the regions around the 21 B. subtilis sites. This suggests that Y complex-dependent processing and, more broadly, mRNA processing in B. subtilis, is more complicated than previously anticipated.","abstract_html":"In Bacillus subtilis, mRNA processing and decay are primarily initiated by the endonuclease RNase Y. Recent work by our group discovered a set of auxiliary factors called the Y complex that is required for the mRNA maturation of 21 operons. It is unclear, however, how these operons specifically are targeted by RNase Y and the Y complex. Here we use in silico sequence motif searches, kmer analysis and secondary structure prediction to analyze these 21 cleavage sites and their surrounding regions. We find enrichment for a guanine immediately preceding the cleavage site. Such enrichment has been previously observed in Staphylococcus aureus RNase Y cleavage sites, indicating a role for the Y complex in processing those sites as well. Surprisingly, there are no other detectable sequence or structural motifs in the regions around the 21 B. subtilis sites. This suggests that Y complex-dependent processing and, more broadly, mRNA processing in B. subtilis, is more complicated than previously anticipated.","abstract_has_math":false,"creators":["Ram, Archana,M. Eng.Massachusetts Institute of Technology."],"institution":"Massachusetts Institute of Technology","degree_name":"Master","degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science","school":null,"contributors":[],"advisors":["Gene-Wei Li."],"committee_chairs":[],"committee_members":[],"year":2020,"date_issued":"2020","date_published":"2020","updated_at":"2026-07-22T22:21:10Z","subjects":["Electrical Engineering and Computer Science."],"languages":["eng"],"rights":["MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided."],"rights_urls":["http://dspace.mit.edu/handle/1721.1/7582"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/1721.1/129913","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Gene-Wei Li."]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. 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Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://dspace.mit.edu/handle/1721.1/7582"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/1721.1/129913"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, February, 2020","Cataloged from student-submitted PDF of thesis.","Includes bibliographical references (pages 75-85)."]},{"key":"dc:description.abstract","label":"Abstract","values":["In Bacillus subtilis, mRNA processing and decay are primarily initiated by the endonuclease RNase Y. Recent work by our group discovered a set of auxiliary factors called the Y complex that is required for the mRNA maturation of 21 operons. It is unclear, however, how these operons specifically are targeted by RNase Y and the Y complex. Here we use in silico sequence motif searches, kmer analysis and secondary structure prediction to analyze these 21 cleavage sites and their surrounding regions. We find enrichment for a guanine immediately preceding the cleavage site. Such enrichment has been previously observed in Staphylococcus aureus RNase Y cleavage sites, indicating a role for the Y complex in processing those sites as well. Surprisingly, there are no other detectable sequence or structural motifs in the regions around the 21 B. subtilis sites. This suggests that Y complex-dependent processing and, more broadly, mRNA processing in B. subtilis, is more complicated than previously anticipated."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["M. Eng."]},{"key":"dc:title","label":"Title","values":["Diverse primary and secondary structural features are associated with Y complex-dependent mRNA maturation in B. subtilis"]}]}],"canonical_facts":{"dc:contributor.advisor":["Gene-Wei Li."],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science","EECS"],"dc:contributor.other":["Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science."],"dc:creator":["Ram, Archana,M. Eng.Massachusetts Institute of Technology."],"dc:date.accessioned":["2021-02-19T20:53:34Z"],"dc:date.available":["2021-02-19T20:53:34Z"],"dc:date.issued":["2020"],"dc:description":["Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, February, 2020","Cataloged from student-submitted PDF of thesis.","Includes bibliographical references (pages 75-85)."],"dc:description.abstract":["In Bacillus subtilis, mRNA processing and decay are primarily initiated by the endonuclease RNase Y. Recent work by our group discovered a set of auxiliary factors called the Y complex that is required for the mRNA maturation of 21 operons. It is unclear, however, how these operons specifically are targeted by RNase Y and the Y complex. Here we use in silico sequence motif searches, kmer analysis and secondary structure prediction to analyze these 21 cleavage sites and their surrounding regions. We find enrichment for a guanine immediately preceding the cleavage site. Such enrichment has been previously observed in Staphylococcus aureus RNase Y cleavage sites, indicating a role for the Y complex in processing those sites as well. Surprisingly, there are no other detectable sequence or structural motifs in the regions around the 21 B. subtilis sites. This suggests that Y complex-dependent processing and, more broadly, mRNA processing in B. subtilis, is more complicated than previously anticipated."],"dc:description.degree":["M. Eng."],"dc:identifier.uri":["https://hdl.handle.net/1721.1/129913"],"dc:language.iso":["eng"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Electrical Engineering and Computer Science."],"dc:title":["Diverse primary and secondary structural features are associated with Y complex-dependent mRNA maturation in B. subtilis"],"dc:type":["Thesis"],"thesis:degree_name":["Master"]},"updated_at":"2026-07-22T22:21:10Z"}