It’s too bad that a little RNA interference (RNAi) won’t quiet down those noisy neighbors, but apparently it does the job quite well on yeast heterochromatin. Researchers from Cold Spring Harbor report that RNAi helps promote the silencing of heterochromatin during DNA replication (“S” phase), and they figured out how it all goes down in their latest paper.
The CSH team ran lots of PCR, sequencing, ChIP, and ChIP-seq experiments in wild-type and mutant yeast cells, in which they found:
- Without RNAi, transcription termination was inefficient in heterochromatin that was around the centromeres, or the middles, of chromosomes. Polyadenylation wasn’t efficient, either. RNA polymerase II (Pol II) also continued to read through the heterochromatin in the absence of RNAi.
- But there was lots of siRNA in wild-type cells in the places where Pol II was released.
- Without RNAi, the DNA repair machinery appeared on the heterochromatin, so it looks like RNAi prevents DNA damage when cells are dividing.
The researchers came up with a model, which they tested with several methods. In the model, modified histones recruit various proteins that promote DNA replication and more histone modification in the heterochromatin. If transcription is happening during S phase, then the replication fork stalls.
There’s some competition between transcription and replication, but if lots of siRNA are around, then Pol II pops off, replication continues, and histones keep getting modified. Without siRNA, however, Pol II just sits there, which tells the cell that the DNA is damaged. So, homologous recombination repairs the DNA, but in the process, some of the modified histones go missing.
For more details, quietly read the full article in Nature, October 2011.