Thesis Defense Announcement
To: The George Mason University Community
Candidate: Anima Sharma
Program: Master of Science in Biology
Date: Monday April 22, 2013
Time: 3:00 p.m.
Place: George Mason University,
Research I, Room 161
Title: "A Study of RNA Editing in Human Plasmacytoid Dendritic Cells and Endotheliocytes by NextGen Sequencing"
Thesis Director: Dr. Ancha Baranova
Thesis Committee: Dr. Deborah Polayes, Dr. Aybike Birerdinc
A copy of the thesis will be available in the Johnson Center Library. All are invited to attend the defense.
RNA editing is a process of post-transcriptional modification of the nucleotide sequence in a transcript that leads to a change in the information content of the RNA. The alteration of nucleotides in the mRNA can have several consequences at the molecular level, including modified protein products as well as creation or deletion of splice sites. Two types of RNA editing have been known to take place in mRNA: Adenosine (A) to Inosine (I) and Cytidine (C) to Uridine (U), both of which involve deamination of the nucleotide with the help of deaminase enzymes. The A to I RNA editing is facilitated by deaminating enzymes known as ADARs (Adenosine Deaminase that Act on RNA). ADARs specifically recognize double stranded RNA structure or RNA duplex structure as their substrate. Though previous studies have shown some evidence of some low level sporadic occurrence of RNA editing in other human tissues, brain remains to be the only tissue where RNA editing has been studied systematically. In this study, we investigated A to I RNA editing in human PDCs (Plasmacytoid Dendritic Cell) capable of producing type I interferons. We were also interested in looking at RNA editing in the umbilical endotheliocytes that are also capable of producing interferons. In this study, the cDNA derived from PDC cells and endothelial cells, was sequenced by NextGen sequencing and the PDC genomic DNA was sequenced by Sanger sequencing and the sequences were analyzed. Since inosine is recognized as guanosine (G) by most enzymes, A-to-I substitution leads to A-to-G transition in the edited substrate and therefore, any kind of A to I RNA editing event will be detected as A to G changes in the transcripts. The multiple sequence alignment tool SeqmanPro was used to assemble all the transcripts together, which revealed that the A to G change frequency was significantly high over 14% in TLR2 at a specific site, in most of the samples of PDCs and endotheliocytes. At the same consensus position 26, the PDCs genomic DNA possessed an Adenosine, which was confirmed by the distinct peak in the chromatogram obtained from Sequencher software. The presence of these A to G mismatches within the transcripts, therefore, suggests that A to I RNA editing takes place in PDCs and endothelial cells.