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Date of Award

Summer 8-15-2019

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Genetics & Genomics)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The development of complex multicellular body plans relies on the differentiation of distinct cell types. These cell types establish the foundation for the construction of elaborate tissue and organ systems that create structural and functional complexity. Cell-type differentiation has evolved repeatedly across multicellular lineages; however, the evolutionary origins of this innovation are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple division of labor between two cell types: germ cells called gonidia and terminally differentiated somatic cells. In this dissertation, I use two complementary approaches to characterize the gene regulatory networks controlling cell-type differentiation in Volvox. I then compare these networks to orthologous gene regulatory networks in the single-celled relative Chlamydomonas reinhardtii to interrogate the evolutionary origins of the cell-type differentiation program in this green algal lineage. In the first approach, I conducted a comprehensive transcriptomic analysis of the gonidial and somatic cell types of Volvox. Over 40% of Volvox genes were found to be expressed in a cell-type-regulated manner. Somatic cells expressed a more specialized genetic program overrepresented in younger, lineage-specific genes, while gonidial cells expressed a more generalist genetic program overrepresented in more ancient genes. Directed analyses of metabolic pathways revealed that gonidial cells preferentially express genes involved in carbon storage accumulation and cell growth, whereas somatic cells express an altruistic metabolic program geared towards the assembly of flagella and the biosynthesis and secretion of extracellular matrix material. Strikingly, I discovered a strong relationship between cell-type gene expression in Volvox and diurnal gene expression in the single-celled relative Chlamydomonas reinhardtii. Volvox orthologs of Chlamydomonas light-phase genes were preferentially expressed in gonidial cells, whereas Volvox orthologs of Chlamydomonas dark-phase genes were preferentially expressed in somatic cells—a result that is consistent with cell-type programs in Volvox arising by co-option of temporal/environmental regulons in a unicellular ancestor. Together, my findings reveal fundamental molecular, metabolic, and evolutionary mechanisms that underlie the origins of cell-type differentiation in Volvox and provide a template for understanding the acquisition of cell-type differentiation in other multicellular lineages. In the second approach, I began to characterize the gene regulatory network under the control of the RegA transcription factor. Maintenance of the somatic cell fate in Volvox is controlled by the regA locus, such that regA- somatic cells will dedifferentiate and redifferentiate as reproductive gonidial cells. The regA gene encodes a putative transcription factor that contains a conserved VARL domain, which harbors a SAND DNA-binding domain. I used DNA affinity purification sequencing (DAP-seq) to identify the candidate genomic binding sites of the RegA VARL domain. The VARL domain bound >1,000 candidate sites across the Volvox genome. Genes neighboring candidate VARL binding sites were enriched for somatic-specific genes. The VARL domain preferentially bound the DNA sequence TTCGA, which is similar to the DNA-binding motifs of SAND domain proteins in other species. The VARL binding motif was enriched near the transcription start sites of somatic-specific genes, suggesting the possibility that RegA functions as an activator of somatic-specific gene expression rather than as a repressor of gonidial-specific gene expression. This work has yielded insights into the DNA-binding properties of RegA and how RegA controls the gene regulatory network underlying somatic cell differentiation in Volvox. Taken together, the findings of this dissertation expand our understanding of the gene regulatory network underlying cell-type differentiation in Volvox and shed light on how this network evolved during the transition from unicellular to multicellular organisms.


English (en)

Chair and Committee

James G. Umen

Committee Members

Douglas Chalker, Susan Dutcher, Dmitri Nusinow, David Queller,


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Available for download on Tuesday, August 15, 2119