Upstream Transcription: A whole lotta stuff going on

Here I am, in the lab with one last experiment to go before I leave to feast on a Christmas Eve dinner, so while I wait for that last centrifugation step, I'll write a quick post about all these great papers on RNA Polymerase II and chromatin remodelling. As I've said before, if you want to understand what is going on with all of these non-coding RNA transcripts, you have to understand how DNA is organized.

If you don't understand how DNA is packed in the typical eukaryotic (i.e. nucleated) cell, please read this:
How Transcription Affects Genomic Organization and Vice Versa
Then to get you up to speed on the latest findings, read this:
Activating a gene through pioneer transcripts

Now, on to the new stuff.

Since I'm pressed for time I'll just point out a few manuscripts that appeared in the past month that indicate how widespread transcription throughout the genome affects the packing of DNA which ultimately affects the expression of protein-coding genes.

Jonathan Houseley, Liudmilla Rubbi, Michael Grunstein, David Tollervey, Maria Vogelauer
A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster
Mol Cell (08) 32:685-695

Bottom line: upstream transcription affects histone modifications that help to regulate the Gal gene promoter.

Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen, Marianne S. Christensen, Christophe K. Mapendano, Mikkel H. Schierup, and Torben Heick Jensen
RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters
Science (08) 322:1851-1854

Bottom line: when you deplete the nuclear exosome (the main RNA degradation machine in the eukaryotic nucleus), all of these "upstream" transcripts appear, both sense and anti-sense. The authors speculate that this has something to do with gene activation.

Yiping He, Bert Vogelstein, Victor E. Velculescu, Nickolas Papadopoulos, and Kenneth W. Kinzler
The Antisense Transcriptomes of Human Cells
Science (08) 322:1855-1857

Bottom line: The authors report that almost half of all genes produce anti-sense transcripts. From the paper:

The distribution of antisense transcripts was distinct from that of sense transcripts, was nonrandom across the genome, and differed among cell types.

Laura Milligan, Laurence Decourty, Cosmin Saveanu, Juri Rappsilber, Hugo Ceulemans, Alain Jacquier, and David Tollervey
A Yeast Exosome Cofactor, Mpp6, Functions in RNA Surveillance and in the Degradation of Noncoding RNA Transcripts
MCB (08) 28:5446-5457

Bottom line: again the depletion of that same exosome complex results in the appearance of ncRNAs. But the authors also find that the exosome component Rrp6 also genetically interacts with mRNA export factors!

And hot off the press:

Thomas S. Ream, Jeremy R. Haag, Andrzej T. Wierzbicki, Carrie D. Nicora, Angela Norbeck, Jian-Kang Zhu, Gretchen Hagen, Thomas J. Guilfoyle, Ljiljana PaÅ¡a-ToliÄ, and Craig S. Pikaard
Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II
Mol Cell (08) Advanced online publication

I haven't had the time to fully digest what's in this paper, but here's the abstract:

In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, abbreviated as Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. We show that Arabidopsis Pol IV and Pol V are composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Four subunits of Pol IV are distinct from their Pol II paralogs, six subunits of Pol V are distinct from their Pol II paralogs, and four subunits differ between Pol IV and Pol V. Importantly, the subunit differences occur in key positions relative to the template entry and RNA exit paths. Our findings support the hypothesis that Pol IV and Pol V are Pol II-like enzymes that evolved specialized roles in the production of noncoding transcripts for RNA silencing and genome defense.


It's looking more and more like the act of transcribing RNA deeply affects how DNA is packed especially with respect to histone modification. In many ways, this cross talk between RNA polymerase and chromatin organization, has been known for a while, but it is becoming increasingly clear that this activity is occurring throughout the entire genome.

Now the questions become

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 degredation 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.

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Great piece on the incredibly complexity of transcription. Also really enjoyed the background links.

"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"?

To add related thought - might the Arabidopsis polIV and polV -derived transcripts be less susceptible to exosome-mediated degradation in the nucleus? Nominally, these enzymes seem to produce primarily nc-like RNAs, but these RNAs must be abundant enough to function in silencing.

It's fun to think about, to be sure.

"2) how do the splicing and RNA nuclear export machineries "know" which transcripts are the real thing"?


Wow! Thanks. A great compilation. I appreciate how you gave the bottom-line for each one.

Thanks for the update. I am always interested in RNA degradation :0

By Marguerite McDonald (not verified) on 30 Dec 2008 #permalink