Cryptosporidium parvum is an important protist pathogen that causes the diarrheal disease cryptosporidiosis in humans and animals. Cryptosporidiosis is waterborne and poses a significant threat to public health globally. While there has been some progress towards understanding the biology of this parasite, gene regulation remains understudied. Non-coding RNA (ncRNA) is a critical regulator of gene expression in eukaryotes at levels of transcription, post-transcription, and translation. Based on transcript length, ncRNAs are classified as small ncRNA (sncRNA, <200 nt) and long ncRNA (lncRNA >200 nt). NcRNA in protist parasites has been gaining attention in recent years as a result of the roles they play in parasite development and host-parasite interactions. Studies from related protist parasites in the phylum Apicomplexa, including Toxoplasma gondii and the malaria parasite Plasmodium falciparum, have demonstrated the pervasive transcription of ncRNA in those species and their interaction with both transcriptional and epigenetic machinery. Very few studies, however, have investigated ncRNA in C. parvum. My research fills this gap by providing a genome-wide systematic annotation of ncRNAs using high-throughput stranded RNA sequence data.

Chapter 1 introduces the fundamental biology of C. parvum and ncRNAs. In chapter 2, the studies of lncRNA and sncRNA in the Apicomplexa over the past decade are reviewed, with a focus on three species: Toxoplasma, Plasmodium and Cryptosporidium. Chapter 3 provides analysis and characterization of small to intermediate size ncRNAs in C. parvum resulting from small RNA sequencing. Chapter 4 examines and characterizes lncRNA transcription using stranded RNA-Seq from multiple lifecycle stages in C. parvum. The limitations and future directions of this field are discussed in Chapter5.