Tudor5-like localizes to a novel germline cytoplasmic RNA granule important for post-transcriptional gene regulation in Drosophila melanogaster

One family of proteins that is known to play a vital role in germline development are the tudor-domain-containing proteins. Previous work in our lab identified a novel tudor-domain protein in Drosophila named Tudor5-like (Tdrd5l) that was capable of promoting male identity in the germline. In this dissertation I focused on understanding how Tdrd5l functions in the germline, and I identified an unexpected role for Tdrd5l in female germline development. Most Tudor-domain-containing proteins function in an RNA metabolism pathway. In the germline many of these tudor proteins function in piRNA biogenesis and localize to an RNA granule called the nuage. Here we found that Tdrd5l localizes to a potentially novel RNA granule, unlike its closest homologues which localize to the nuage and repress transposons. The Tdrd5l granule we observe associates with the nuage and processing body but doesn’t perfectly co-localize. Additionally, Tdrd5l granules are much larger than most characterized RNA granules. Lastly, we found that like many tudor proteins, Tdrd5l functions in post-transcriptional gene regulation based on genetic interaction assays. In the female germline we found that Tdrd5l regulates a special type of RNA called maternally deposited RNAs. In this study we specifically focus on the role Tdrd5l plays in regulating the maternally deposited RNA gurken (grk). My results showed that Grk protein expression is de-repressed in the nurse cells where it is usually silenced. In addition, we observed dorsalized eggs laid by Tdrd5l mutant females, a phenotype that also indicates a defect in grk regulation. To further understand how Tdrd5l regulates Grk protein expression, we tested whether Tdrd5l regulates Orb, which is an activator of Grk translation. We found that Tdrd5l acts to repress Orb in the nurse cells, a mechanism that could explain why Grk is ectopically expressed in Tdrd5l mutants. Overall my data demonstrate that Tdrd5l localizes to a novel RNA granule and that this protein is capable of regulating mRNAs in the female germlin

Tudor5-like localizes to a novel germline cytoplasmic RNA granule important for post-transcriptional gene regulation in Drosophila melanogaster

One family of proteins that is known to play a vital role in germline development are the tudor-domain-containing proteins. Previous work in our lab identified a novel tudor-domain protein in Drosophila named Tudor5-like (Tdrd5l) that was capable of promoting male identity in the germline. In this dissertation I focused on understanding how Tdrd5l functions in the germline, and I identified an unexpected role for Tdrd5l in female germline development. Most Tudor-domain-containing proteins function in an RNA metabolism pathway. In the germline many of these tudor proteins function in piRNA biogenesis and localize to an RNA granule called the nuage. Here we found that Tdrd5l localizes to a potentially novel RNA granule, unlike its closest homologues which localize to the nuage and repress transposons. The Tdrd5l granule we observe associates with the nuage and processing body but doesn’t perfectly co-localize. Additionally, Tdrd5l granules are much larger than most characterized RNA granules. Lastly, we found that like many tudor proteins, Tdrd5l functions in post-transcriptional gene regulation based on genetic interaction assays. In the female germline we found that Tdrd5l regulates a special type of RNA called maternally deposited RNAs. In this study we specifically focus on the role Tdrd5l plays in regulating the maternally deposited RNA gurken (grk). My results showed that Grk protein expression is de-repressed in the nurse cells where it is usually silenced. In addition, we observed dorsalized eggs laid by Tdrd5l mutant females, a phenotype that also indicates a defect in grk regulation. To further understand how Tdrd5l regulates Grk protein expression, we tested whether Tdrd5l regulates Orb, which is an activator of Grk translation. We found that Tdrd5l acts to repress Orb in the nurse cells, a mechanism that could explain why Grk is ectopically expressed in Tdrd5l mutants. Overall my data demonstrate that Tdrd5l localizes to a novel RNA granule and that this protein is capable of regulating mRNAs in the female germlin

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu