Position: Graduate Student
Contact: sboerner@bio.fsu.edu
Education: M.S. in Biological Science (2012), Florida State University
Thesis Title:
Identification and classification of long noncoding RNA in Zea mays using computational and bioinformatic approaches
Thesis Abstract:
Computational analysis of cDNA sequences from multiple organisms suggests that a large
portion of transcribed DNA does not code for a functional protein. As studies begin to delve into
the possible functions of these noncoding transcripts, the results are revealing an ever more
complex genome, where what was once dubbed "junk" is now seemingly necessary. The
characterization of several long noncoding (lnc)RNAs in human and mouse has involved the
analysis of raw genomic sequence data with a set of rules to computationally predict functional
noncoding transcripts; other approaches involve expression datasets from microarray or RNAseq
technology to achieve the same end. As these studies increase, the number of functions, classes
and names, of noncoding transcripts increase as well. Many examples of lncRNAs appear to
have an epigenetic role in humans, including HOTAIR and XIST. While epigenetic gene
regulation is clearly an essential mechanism in plants, relatively little is known about the
presence or function of lncRNAs in plants. To explore the connection between lncRNA and
epigenetic regulation of gene expression in plants, a computational pipeline using the
programming language Python that will identify, classify, and localize potential lncRNAs has
been developed and applied to maize full length cDNA sequences. This analysis revealed that a
large portion of transcribed sequences in maize are not predicted to be coding. In addition, over
half of the predicted noncoding transcripts contain small RNA sequences. Also, approximately
half of the predicted noncoding transcripts are associated with a gene model. Of these, roughly
20 percent are antisense to their host gene loci. Sequence analysis identified a GA rich motif that
is similar to two known motifs in previously charatercterized lncRNAs, roX2 and HOTAIR.
Overall these results suggest that lncRNAs may be a component of genome regulation in maize.