Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Cell & Molecular Biology (PhD)

Degree Level



Biological Sciences


Andy Pereira

Committee Member

Ken Korth

Second Committee Member

Vibha Srivastava

Third Committee Member

Ines Pinto


Biosynthesis, Cell Wall, ChIP-Seq, Rice, RNA-Seq


The plant cell wall is of critical importance to plant growth and survival, functioning in maintaining structural integrity, supporting cell expansion, and acting as the first line of defense in response to biotic and abiotic stresses. The major components of the cell wall are cellulose, hemicelluloses, lignin, and pectin. Recent focus on the transcriptional machinery regulating cell wall biosynthesis in plants has revealed many key transcription factors responsible for orchestrating cell wall deposition. However, many of these TFs act redundantly and work coherently with a suite of TFs to activate the cell wall biosynthetic machinery. Heterologous expression of TFs is an ideal way to characterize the conserved roles of a TF in a pathway.

Here, we investigate the process of cell wall formation in rice by overexpression of the heterologous TF AtSHN2 from Arabidopsis, to unravel the process of cell wall biosynthesis in rice. Using Tandem Affinity Purification (TAP) enabled Chromatin Immunoprecipitation studies coupled with genome-wide sequencing analysis, cis-regulatory elements bound by AtSHN2 were identified. It was identified that AtSHN2 can bind to GCC box elements present in the promoter sequence of the downstream MYB TFs and [GA]CAACA[TG][AT] element specific of AP2 TFs. Furthermore, transcriptomic profiling of AtSHN2-TAP rice transgenic lines was performed to identify direct and indirect global targets of AtSHN2. In addition, this dissertation also characterizes the role of OsSHN2, the ortholog of AtSHN2 from rice in cell wall biosynthesis in rice using transcriptomic studies. Taken together, this dissertation seeks to unravel the mechanism of cell wall formation in rice using global genomic changes associated with AtSHN2 overexpression in rice plants.