Oxytricha trifallax is a stichotrich which transforms a micronucleus into a macronucleus during sexual development by excising and rearranging its DNA. During this genomic rearrangement, more than 90% of the DNA sequence in the micronuclear chromosomes is deleted. The remaining sequences are converted into ~16,000 nanochromosomes with average length of 3 kb, forming the macronucleus. Development of the new macronucleus from a copy of the zygotic micronucleus requires a suite of non-coding RNAs. In Oxytricha trifallax, long RNA templates, together with 27-nucleotide Piwi associated RNAs, guide genome rearrangements. By exploiting these pathways, somatic gene knockouts in Oxytricha have been developed. In this study we investigated two highly expressed early sexual development-specific genes, Alba-like 1 and Alba-like 2, which encode Alba domain containing proteins. Alba domains are known to be nuclei acid binding proteins and are involved in translation regulation in Trypansoma brucei (Mani et al., 2011) and Plasmodium falciparum (Vembar et al., 2015). Both Alba-like 1 and Alba-like 2 genes were identified as co-precipitates of long dsRNA, possibly the RNA templates, in early sexual development. Knockouts of both genes were developed through exploiting the genomic rearrangement pathways of Oxytricha via different approaches. The introduction of artificial piRNAs programs the retention of normally eliminated sequences, which permits retention of DNA sequences that interrupt open reading frames. Another approach is the introduction of synthetic DNA templates which sometimes induces deletion of the targeted nanochromosome. For both genes, the knockout cell lines are viable during vegetative, asexual growth but unable to complete sexual development, with Alba-like 1 being trans-lethal when mated to wild type. To further probe the functions of these target genes, tagged proteins were generated using artificial nanochromosomes injected into the macronucleus of vegetative cells. This transformation approach results in artificial chromosomes that are maintained throughout the asexual life cycle at high copy number and show expression patterns that faithfully recapitulate their native counterparts and permit purification of the tagged proteins. Together, these experiments have increased the utility of Oxytricha trifallax as a model system for genetics.