Convergent transcription, polyadenylation, RNA editing, and regulation

One of the mechanisms by which polyadenylation may contribute to the regulation of gene expression (on paper, at least) involves gene pairs that are situated near each other and transcribed convergently.  In these instances, polyadenylation and transcription termination need to occur to prevent the production of RNAs that are anti-sense to the two members of the convergently-transcribed gene pair.  Overlapping transcripts could lead to the formation of double-stranded RNAs that could in turn trigger regulatory mechanisms, resulting in altered accumulation of the corresponding transcripts.

It is in this vein that a recent study from Gordon Carmichael’s lab at the University of Connecticut is of interest.  Briefly, these authors report that the early-to-late transition in gene expression in cells infected with the mouse polyoma virus is accomplished (at least in part) by a reduction in polyadenylation efficiency of the primary transcript encoding the so-called late genes.  Interestingly enough, this reduction in polyadenylation efficiency seems to be due to A-to-I editing of the region around the polyadenylation signal.  This editing in turn may be traced to an overlap of the early and late transcripts, such that double-stranded RNAs (the substrate for the A-to-I editing complex) that include the late polyadenylation signal are produced and edited before pre-mRNA processing occurs.

SOC1 and the RNA Underworld

Earlier, I described studies of the so-called SOC1 and FUL genes of Arabidopsis, genes that when mutated in concert change the growth habit of the plant is most remarkable ways.  A report that just came up on Plant Cell Online links one of these genes with one of the mechanisms by which RNAs are turned over in the cell.  Briefly, this study reveals that SOC1 expression is subject to posttranscriptional control, and that this control is linked with a component of the machinery that mediates nonsense-mediated decay (NMD) in plants.  This finding may be of interest for a number of reasons.  One is that NMD hasn’t yet been linked with lots of regulation in plants – it occurs, and we may infer conceptual links between alternative RNA processing and NMD, but much remains to be learned.  A second is that SOC1 functioning, previously implicated in important macroevolutionary transitions in plants, may be altered by many evolutionary processes, including those that affect RNA levels through NMD.

The abstract:

SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) is regulated by a complex transcriptional regulatory network that allows for the integration of multiple floral regulatory inputs from photoperiods, gibberellin, and FLOWERING LOCUS C. However, the posttranscriptional regulation of SOC1 has not been explored. Here, we report that EARLY FLOWERING9 (ELF9), an Arabidopsis thaliana RNA binding protein, directly targets the SOC1 transcript and reduces SOC1 mRNA levels, possibly through a nonsense-mediated mRNA decay (NMD) mechanism, which leads to the degradation of abnormal transcripts with premature translation termination codons (PTCs). The fully spliced SOC1 transcript is upregulated in elf9 mutants as well as in mutants of NMD core components. Furthermore, a partially spliced SOC1 transcript containing a PTC is upregulated more significantly than the fully spliced transcript in elf9 in an ecotype-dependent manner. A Myc-tagged ELF9 protein (MycELF9) directly binds to the partially spliced SOC1 transcript. Previously known NMD target transcripts of Arabidopsis are also upregulated in elf9 and recognized directly by MycELF9. SOC1 transcript levels are also increased by the inhibition of translational activity of the ribosome. Thus, the SOC1 transcript is one of the direct targets of ELF9, which appears to be involved in NMD-dependent mRNA quality control in Arabidopsis.

The citation (hopefully, I will remember to update it once the paper comes out in print with the updated link for the paper copy):

Hae-Ryong Song, Ju-Dong Song, Jung-Nam Cho, Richard M. Amasino, Bosl Noh,  and Yoo-Sun Noh. The RNA Binding Protein ELF9 Directly Reduces SUPPRESSOR OF OVEREXPRESSION OF CO1 Transcript Levels in Arabidopsis, Possibly via Nonsense-Mediated mRNA Decay.  Plant Cell Advance Online Publication, Published on April 17, 2009; 10.1105/tpc.108.064774

More strangeness …

Awhile ago, I discussed a flurry of papers in Science that showed some curious aspects of transcription and promoters.  It seems as if every passing day brings a new report that pertains to the phenomenon.  A recent issue of Nature brings us two papers, back to back, that are relevant.  The bottom line is that bidirectional transcription is a widespread phenomenon, at least in yeast.  Moreover, this phenomenon is responsible, not just for divergent transcription of mRNA-encoding genes, but also for the production of so-called Cryptic Unstable Transcripts and other uncharacterized RNAs.  The abstracts and some brief commentary are beneath the fold.

Interesting stuff

While my yard is recovering from the ice, and I from today’s UK game, I thought I would toss out a few interesting abstracts that touch on important and contentious issues.  Peek beneath the fold and, as always, enjoy.

Strange things at promoters

A group of interesting papers popped up on ScienceExpress this past week.  These papers (by Core et al., Seila et al., He et al., and Preker et al.) all describe characterizations of unusual patterns of transcription in human cells.  The bottom line (well, one bottom line – there are lots of interesting data in these studies, and the nuances may take readers in slightly different directions) is that, for numerous promoters, transcription extends in both directions, not just in the one direction that is usually associated with productive (= leading to synthesis of a processed and translated mRNA) transcription.  Moreover, this bidirectional transcription is quite distinct from that associated productive transcription, in that it yields short and relatively unstable RNAs.  More elaboration follows below the fold.  As always, enjoy.

Off with their heads!

As noted in this earlier essay, the poly(A) tail collaborates with the 5′-end of the mRNA (the so-called cap) to promote both mRNA translation and stability.  Accordingly, decapping is a good hallmark for mRNA turnover.  In a recent issue of The Plant Cell, Jiao et al. describe an approach to study uncapped mRNAs on a global basis.  Briefly, these authors take advantage of the fact that an uncapped mRNA has a 5′ phosphate group, and thus can be a substrate for RNA ligase.  By attaching an RNA adapter to the uncapped mRNAs using this enzyme, and then purifying and amplifying DNA products derived from these, the authors were able to prepare probes for microarray studies.  Thus, they were able to assess uncapped mRNA abundance on a genome-wide basis.  As a test for this approach, they studied decapping genome-wide during the early stages of flowering using a mutant arrested for flower development at a specific stage, but carrying a chemically-inducible transgene that could trigger flowering by providing for some of the functionality missing in the mutant.  This group found that a sizable portion of mRNAs that could be detected on the microarrays (approaching 40%) were either “over-capped” or “under-capped”; that is to say, the relative abundances of uncapped mRNAs differed from the total levels of the corresponding transcripts.  They also found a number of transcripts (some 300 or so) whose capping status changed during flowering.  All told, as stated by the authors, this system should be useful for exploring regulated mRNA turnover, and for identifying correlations between mRNA sequence/structure and stability.

The Small RNA World – a brief introduction

The first reflex when coming across the title of this blog is, most likely, that it is a blog that mentions microRNAs and small RNAs. Up until now, I suppose that I’ve been a disappointment, as the scientific focus has been on the subject matter of my lab – polyadenylation. But this changes with this essay, an overview of the field of small RNAs. My goal with this overview is to lay a foundation to which I can refer in other contexts. As always, enjoy (and feel free to ask questions or correct any mistakes you find).

The 2008 Winners

… of the Albert Lasker Basic Medical Research Award are Victor Ambros, David Baulcombe, and Gary Ruvkun.  These scientists are pioneers in the field of small RNAs, and have helped dissect the process in animals and plants.  Some snippets from The Lasker Foundation announcement:

The 2008 Albert Lasker Award for Basic Medical Research honors three scientists who discovered an unanticipated world of tiny RNAs that regulate gene activity in plants and animals. Victor R. Ambros (University of Massachusetts Medical School, Worcester) and Gary B. Ruvkun (Massachusetts General Hospital, Boston, Harvard Medical School) unearthed the first example of this type of molecule in animals and demonstrated how the RNAs turn off genes whose activities are crucial for development. David C. Baulcombe (University of Cambridge) established that small RNAs silence genes in plants as well, thus catalyzing discoveries of many such RNAs in a wide range of living things. His findings led to the identification of the biochemical machinery that unifies numerous processes by which small RNAs govern gene activity.

Ambros, Baulcombe, and Ruvkun did not set out to unveil small regulatory RNAs. Ambros and Ruvkun were studying how the worm Caenorhabditis elegans develops from a newly hatched larva into an adult. Baulcombe, in a seemingly unrelated line of inquiry, was probing how plants defend themselves against viruses. All three investigators possessed the open mindedness, wisdom, and experimental finesse to entertain the possibility—and then verify—that tiny RNAs could perform momentous feats. Their work has led to the realization that these molecules are pivotal regulators of normal physiology as well as disease.

A few paragraphs later:

Across the Atlantic, David Baulcombe, then of the Sainsbury Laboratory in Norwich, UK, was studying how plants resist viruses. When he and others added to viral-infected plants unusual versions of viral genes, the mRNA copies of the normal genes as well as the newly introduced ones disappeared. Similarly, experimentally added non-viral genes suppressed activity of plant genes that contained similar sequences. Baulcombe proposed that such gene silencing occurs when RNAs embrace target mRNA—through typical Watson-Crick base-pairing—and promote destruction of the mRNA or interfere with its translation into protein. However, no one could find such RNAs.

Baulcombe reasoned that the predicted RNAs might have eluded researchers because the molecules were shorter than anyone imagined and thus, experiments had not been designed to detect them. In 1999, he and a postdoctoral fellow in his laboratory, Andrew Hamilton, devised a hunt specifically for small RNAs. They added test genes to plants and found 25-nt long RNAs that matched; furthermore, these small RNAs appeared only under conditions in which target mRNA activity was shut off. The stunning similarity in size between the plant and worm RNAs suggested that small regulatory RNAs exist in many organisms. Furthermore, it hinted at the presence of cellular machinery that dedicates itself to creating these precisely sized molecules and then uses them to quash gene activity.

Readers are encouraged to read the paper by Hamilton and Baulcombe that started to reveal the true scope of the RNA Underworld.  And another paper from Baulcombe’s group that ties in an underlying theme of this blog to the subject of small RNAs and silencing.  As always, enjoy.

The nuclease aisle

One of the themes that keeps popping up here is that of nucleases.  I thought I would post an adaptation of a table from a recent review by Ciarán Condon that lists the various ribonucleases in E. coli and B. subtilis.  The point is to illustrate the variety of nucleases that exist in bacteria, and to get readers to think more of the importance of RNA processing and, moreso, RNA turnover.

This table is adapted from Condon C (2007), Maturation and degradation of RNA in bacteria, Current Opinion in Microbiology 10: 271–278.  Enjoy.

One person’s junk is another’s treasure

In previous essays (here and here), we learned that genes encoding new proteins can and do, often, arise de novo in the course of evolution, contradicting one of the central tenets of ID proponents.  The means by which these genes arise are many.  One of these, suggested by Cai at al. (the subject of one of the earlier essays), involved the adaptation of a gene encoding an evolutionarily-conserved non-coding RNA via the appearance, by mutation, of appropriate translation initiation and termination (“start” and “stop”) codons.  This mechanism represents an intersection of sorts between the subject of protein evolution and another matter of discussion on these blogs, namely the existence, evolution, and “function” of junk DNA.  In this essay, I review a 2007 study by Debrah Thompson and Roy Parker (“Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae”, Mol. Cell. Biol. 27, 92-101) that adds a great deal of clarity to this mode of gene and protein evolution.