Hoe, Chee Hock
(2013)
Experimental Rnomics:
The Identification And
Characterization Of Small
Non-Protein-Coding Rna (Npcrna) In
Vibrio Cholerae.
PhD thesis, Universiti Sains Malaysia.
Abstract
Non-protein-coding RNAs (npcRNAs) are RNA that are not translated into
protein but are involved in a myriad of cell regulatory processes including
orchestrating bacterial general stress responses and bacterial virulence. The
identification and characterization of npcRNAs from the etiologic agent of cholera,
Vibrio cholerae (V. cholerae) El Tor, was reported in this study. Using experimental
RNomics approaches, 224 npcRNA candidates have been identified; 92 belong to the
class of putative cis-antisense npcRNAs, whereas 132 are the intergenic npcRNAs.
Among these npcRNA candidates, differential expressions for 56 of them could be
verified via Northern blot analysis. Parallelly, 627 npcRNA candidates were reported
by another group in a transcriptomic profile survey in V. cholerae El Tor N16961
using RNA-seq. Intriguingly, only 39 npcRNA candidates were common to both
datasets. A series of defined tests prompted that RNA substrate, phosphorylation
status, C-tailing, adapter ligation, and different sequence of adapter are significant
sources of the bias between conventional sequencing and deep sequencing. This
suggested that the data in our study is valid and further characterization of the
npcRNA candidates was carried out. Two intergenic npcRNA genes were developed
as potential diagnostic markers, which could in a multiplex PCR assay serve to be an
important tool in molecular epidemiological studies of V. cholerae.
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