A Motif Discovery and Analysis Pipeline for Heterogeneous Next-Generation Sequencing Data

Bioinformatics has made great strides in understanding the regulation of gene expression, but many of the tools developed for this purpose depend on data from a limited number of species. Despite their unique genetic attributes, there remains a dearth of research into undomesticated trees. The poplar tree, Populus trichocarpa, has undergone multiple rounds of genome duplication during its evolution. In addition its life cycle varies from other annual crop and model plants previously studied, leading to significant technical challenges to understand the unique biology of these trees. For example, the process of secondary growth occurs as the tree stems thicken, and creates secondary xylem (wood) and phloem (inner bark) for water and products of photosynthesis transport, respectively. Because of this, the research group I work with studies the secondary growth of P. trichocarpa (Spicer, 2010) (Groover, et al., 2010) (Groover, et al., 2006) (Groover, 2005). The genomic tools to investigate gene regulation in P. trichocarpa are readily available. Next-generation sequencing technologies such as RNA-Seq and ChIP-Seq can be used to understand gene expression and binding of transcription factors to specific locations in the genome. Similarly, a variety of specialized bioinformatic tools such as EdgeR, Cufflinks, and MACS can be used to analyze gene binding and expression from sequencing data provided by ChIP-seq and RNA-seq (Blahnik, et al., 2010) (Mortazavi, et al., 2008) (Robinson, 2010) (Robinson, 2007) (Robinson, et al., 2008) (McCarthy, 2012) (Trapnell, 2013) (Zhang, 2008). The binding and expression data these tools provide form a foundation for analyzing the gene expression regulation in P. trichocarpa. The goal of my project is to provide a motif discovery and analysis pipeline for analyses of Populus species. The motif discovery and analysis pipeline utilizes heterogeneous data collected from poplar and aspen mutants to elucidate the gene regulatory mechanisms involved in secondary growth. The experiments target transcription factors related to secondary growth, and through analysis of the variety of transcription factor binding experiments, I have identified the motifs involved in gene regulation of secondary growth within P. trichocarpa. (Filkov, et al., 2008)