BMCB625:Noncoding Y RNA

(Homework) Questions

Larry

---

Chayne

---

Jon

Q1: How do the authors proove that human Y RNAs are necessary for semiconserative chromosomal DNA replication.

A1: BrdU triphosphate and density gradient centrifugation (old school!)

Q2: How might you find protien partners for Y RNAs assuming they are ribonuclearproteins.

A1: Fishing with radiolabled Y RNA as bait out from your extracts. gel shift etc.

---

Chris

There appears to be a bulge in the stem structure of Y-RNA’s similar to that present in IRE’s (Iron Responsive Elements); in IRE’s this “stem-bulge” is critical for recognition by the Iron-Responsive Protein (IRP).

Does the bulge on the stem structure serve a specific a function in Y-RNA’s? (First off, is it real, and conserved? The "CG-bulge" is most frequently mutated in psuedogene Y-RNA (Perreault, et al., Nucleic Acids Res. 2005; 33(6): 2032–2041).

Structurally, this could be tested with a variety of Nuclease treatments. e.g., RNase V1 (dsRNA), RNase T1 (ssG), RNaseA (ssU & ssC)). Does mutation of this C-bulge change the binding/association with Ro? Any other ideas for testing experimentally?

---

Jeremy

Q1. The authors propose that the Y RNAs guide the formation of specific RNP complexes by strand hybridization and that these complexes are necessary for DNA replication. How might you identify nucleic acids which hybridize to a Y RNA?

Q2. How could you test the physiological importance of hybridization between Y RNA and it's target nucleic acid?

Hint: The paper I will be presenting uses some of these techniques to study BC1 RNA.