Molecular and evolutionary properties of non-gene-coding regions in bacteria using comparative genome bioinformatics
Item
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Title
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Molecular and evolutionary properties of non-gene-coding regions in bacteria using comparative genome bioinformatics
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Identifier
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d_2009_2013:e10911eedf23:10421
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identifier
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10570
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Creator
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Sukarna, Tika Y.,
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Contributor
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Weigang Qiu
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Date
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2010
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Language
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English
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Publisher
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City University of New York.
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Subject
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Evolution & development | Molecular biology | Bioinformatics | Bacteria | Borrelia | Comparative Genomics | Evolution | Intergenics | Noncoding
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Abstract
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Although most nongenecoding regions of the genome have long been thought of as nonfunctional, a growing body of literature now show that many sites act as important sources of phenotypic variation and complexity. In eukaryotes, this has been attributed to the sophisticated gene regulatory apparatus that includes cisacting regulatory elements acting on multiple levels. In bacteria, this level of regulatory multiplicity is reduced, as is reflected by the lower percentage of intergenic segments in their genomes and the lower capacity for metabolic and catabolic activities. Most nongenecoding intergenic portion of the genome of bacteria is thought of as functionally compact, mostly transcriptional and translational regulatory in nature, containing only limited number of infrastructural or regulatory RNAs. This study addresses the extent of this cisregulatory organization on noncoding genomic regions in the Lyme bacteria Borrelia burgdorferi as apparent in their molecular and evolutionary properties and how they can influence and be applied to the bioinformatic predictions of cisregulatory function. Several general molecular and evolutionary properties of a bacterial noncoding genome were identified. Overall, most nongenecoding intergenic portion of Borrelia are constrained, functionally compact and degenerate. A phylogenetic footprinting approach for very closely related species (> 90% nucleotide sequence identity) was developed to test for specific sites of transcriptional regulation, which was additionally tested using the Escherichia coli genome dataset. The method finds most constrained regions to coincide with several general properties of promoter binding, suggesting that constraint levels are differentiable even amongst these very closely related bacterial species, providing a way to measure for molecular function at a fine phylogenetic level through the understanding of the patterns of DNA sequence evolution.
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Type
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dissertation
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Source
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2009_2013.csv
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degree
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Ph.D.
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Program
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Biology
