Topics for Further Research

Alex Palazzo rounds up some new papers on transcription and he says this recent research is showing that crosstalk between RNA polymerase and the organization of chromatin is widespread in the genome. Now, he says, the questions are:

1) how does the RNA degradation machinery "know" which transcript is the nc-RNA byproduct of this cross-talk and thus a substrate for degradation
2) how do the splicing and RNA nuclear export machineries "know" which transcripts are the real thing! We have pretty good evidence that these filters work very well in eukaryotes and there is a lot of genetic evidence that the RNA degradation machinery and the histone modification machinery communicate somehow to the proteins involved in mRNA nuclear export. This RNA filtering process is one of the main differences between euks and proks. But that filter is looking more and more mysterious.