2026-09-19T20:27:39Zhttps://dspace.mit.edu/server/oai/requestoai:dspace.mit.edu:1721.1/1299132026-06-06T00:49:16Zcom_1721.1_7582com_1721.1_7581col_1721.1_131023
Gene-Wei Li.
Ram, Archana,M. Eng.Massachusetts Institute of Technology.
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
2021-02-19T20:53:34Z
2021-02-19T20:53:34Z
2020
2020
https://hdl.handle.net/1721.1/129913
1237530663
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).
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.
by Archana Ram.
M.Eng.
M.Eng. Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science
85 pages
eng
Massachusetts Institute of Technology
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.
http://dspace.mit.edu/handle/1721.1/7582
Electrical Engineering and Computer Science.
Diverse primary and secondary structural features are associated with Y complex-dependent mRNA maturation in B. subtilis
Thesis
application/pdf
2021-02-19T20:53:04Z
Publication
Master
EECS
unknown
unknown
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<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>
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