Non-Coding Genomics of Methanocaldococcus Jannaschii: A Survey of Promoters, Non-Coding RNA Genes, and Repetitive DNA Elements
Li, Enhu
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https://hdl.handle.net/2142/84848
Description
Title
Non-Coding Genomics of Methanocaldococcus Jannaschii: A Survey of Promoters, Non-Coding RNA Genes, and Repetitive DNA Elements
Author(s)
Li, Enhu
Issue Date
2007
Doctoral Committee Chair(s)
Gary Olsen
Department of Study
Biochemistry
Discipline
Biochemistry
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biology, Molecular
Language
eng
Abstract
Non-protein-coding sequences of a genome carry out various tasks which contribute to the functionality of the genome as an information carrier. They are essential genomic components and are operative in genetic information remission, transfer, and processing---key processes where the three domains of life, Bacteria, Archaea, and Eucarya, differ from one another. This thesis focuses on some non-coding features of an archaeal genome, that of Methanocaldococcus jannaschii, in an effort to identify and characterize promoters, non-coding RNA genes, and novel repetitive DNA sequences. Genome-wide identification of transcription factor binding sites revealed archaeal core promoter elements, which include TATA box, BRE, and an initiator element. The structural similarity between archaeal basal promoters and those from Eucarya has reinforced the relationship between them. A quantification of transfer RNA (tRNA) abundance showed a correlation between codon usage frequency and the intracellular cognate tRNA concentration in this organism. Further characterization of tRNA gene promoters indicated that a key determinant of tRNA expression levels is the differential affinity of transcription factors to various tRNA gene promoters. The whole genome approach of promoter searching also led to the identification of several non-coding RNA genes. Nonprotein-coding RNA (ncRNA) promoters share the same set of core elements but with more deviations from the consensus compared to those of tRNA genes; in accordance, they possess lower affinity to the transcription factors. Some additional ncRNA transcripts were isolated in M. jannaschii; they are located in intergenic or intragenic regions, and encoded sense or antisense relative to the surrounding or enclosing genes. These novel transcripts further confirm the high abundance and diversity of ncRNA genes in this genome. Lastly, groups of novel repetitive DNA elements (nontandem short repeat, NTSR) were identified in M. jannaschii, by a search strategy which combines sequence and secondary structure information. These NTSRs share essential characters similar to bacterial REPs, in terms of the abundance, G+C content, structure, and genome-wide location.
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