Cleveland Rocks!

October 30, 2010

Not just the Rock and Roll Hall of Fame.  Last weekend, a group of midwestern RNA scientists gathered for the annual Rustbelt RNA Meeting in Cleveland. (There’s a clever pun hidden in the name, one that may fall by the wayside in the next year or so.)

Here is a link to the abstracts.  So readers can take a peek into just what excites RNA scientists.  Enjoy.

PS – just out of curiosity, does the name “Rustbelt” carry negative connotations for readers here?  Just wondering.

Now that’s a streamlined NIH grant proposal

October 20, 2010

Rocket Boys.  Enjoy.


October 20, 2010

No, it’s not about the rock band.  Nor is it about sleep physiology.  Rather, this short blurb is intended to point out a recent review in Trends in Biochemical Sciences that ties together a long trickling of research extend back for many decades.

For at least 20 years, it has been known that a number of enzymes that catalyze reactons in intermediary metabolic pathways are also RNA binding proteins.  The “classical” case is that of aconitase.  This enzyme catalyzes the isomerization of citrate to isocitrate, a reaction that is part of the tricarboxylic acid cycle.  The enzyme also binds the so-called iron-responsive element in mRNAs, and in so doing regulates RNA stability and translation.  Aconitase activity and RNA binding are mutually exclusive, and the role the protein plays depends on teh iron status of the cell.

Similar RNA-binding moonlighting has since been shown for a number of other enzymes.  I won’t list them here – the review does a nice job of this.  The review also discusses the possible integration of metabolic cues with RNA homeostasis.  It doesn’t touch on a more fascinating topic – the possibility that RNA binding may be a vestige of the deep past, reflecting the possibility that, at one time, all proteins may have interacted with RNA or been involved with RNA metabolism in some way.  But the latter is a subject that better left for another review.

Read the rest of this entry »

Plants are people too!

October 18, 2010

The first sentence from a recent paper in RNA:

Noncoding RNAs (ncRNAs) are widespread transcripts occurring from yeast to human, but their functions remain unclear (Kapranov et al. 2002; Rinn et al. 2003; Yelin et al. 2003; Cheng et al. 2005; Davis and Ares 2006;Neil et al. 2009).

Um, what the heck! ncRNAs have been known in plants for quite some time – at least 5 years.

Oh well.  The paper itself is interesting – talking about how short intragenic RNAs* modulate transcription of their associated gene.  The suggestion (based on experimental data) that the specific ncRNAs in this case are not transcribed by polII adds yet one more twist to the interconnections between polymerases, chromatin modifications, and regulation.

And, yes, it’s almost for certain that these things happen in plants.

The abstract:

Inter- and intragenic noncoding transcription is widespread in eukaryotic genomes; however, the purpose of these types of transcription is still poorly understood. Here, we show that intragenic sense-oriented transcription within the budding yeast ASP3 coding region regulates a constitutively and immediately accessible promoter for the transcription of full-length ASP3. Expression of this short intragenic transcript is independent of GATA transcription factors, which are essential for the activation of full-length ASP3, and independent of RNA polymerase II (RNAPII). Furthermore, we found that an intragenic control element is required for the expression of this noncoding RNA (ncRNA). Continuous expression of the short ncRNA maintains a high level of trimethylation of histone H3 at lysine 4 (H3K4me3) at the ASP3 promoter and makes this region more accessible for RNAPII to transcribe the full length ASP3. Our results show for the first time that intragenic noncoding transcription promotes gene expression.

The citation and link:

Huang YC, Chen HT, Teng SC. 2010. Intragenic transcription of a noncoding RNA modulates expression of ASP3 in budding yeast. RNA 16, 2086-2093.

* – short intragenic RNAs are non-coding RNAs (ncRNAs) that are transcribed from within a larger gene or transcription unit.  The ones described in this report are in the sense orientation, but antisense short intragenic ncRNAs are also possible.

I didn’t know it could do this ….

October 8, 2010

What better way to cut short this unanticipated hiatus (no real reason – just got busy with other stuff) than point readers to a new study that reveals yet another unexpected and unusual property of a plant polyadenylation factor subunit.  In a nutshell (which is posted, as the abstract, beneath the fold), Balu Addepalli has found that two of the cysteines in one of the three CCCH zinc finger motifs in the Arabidopsis CPSF30 protein (that’s a mouthful) are actually engaged in a disulfide bond.  This was unexpected (to me, at least) because it is usually assumed that the cysteines and histidine residue coordinate around a zinc ion (hence the term zinc finger).  As indicated in the abstract, this new finding raises the possibility that the Arabidopsis CPSF30 is regulated in part by redox control, through oxidation and reduction of the disulfide bond.

So, this adds one more item to the cart of novelties regarding the plant CPSF30.  The gene encoding the protein is alternatively spliced, such that the CPSF30 part of the resulting protein is fused to a novel, poorly-understood domain.  (See this article for the details.)  The protein is not essential for growth (in contrast to its yeast counterpart, Yth1p).  CPSF30 mutants (we call them oxt6 mutants) are tolerant to oxidative stress.  (This may be relevant to the disulfide linkage story – future research will tell).  The Arabidopsis CPSF30 is an endonuclease, an activity for which a function has not been firmly established (although my group thinks we know – see this study).  This protein is also a calmodulin-binding protein, which raises interesting possibilities concerning regulation, signaling, and polyadenylation. Read the rest of this entry »