Just how widespread is alternative polyadenylation in plants?

November 14, 2012

This is the question I think about a lot, and one I spent a some time on in a recent minireview.  The answer is, in a nutshell, very.

One of the things I had to do for this review was try and make sense out of the different approaches that have been described recently for studying alternative poly(A) site choice in plants.  One of these – the use of high-throughput sequencing to sequence cDNA tags that query the exact mRNA-poly(A) junction – has been discussed previously, in a general sense and in terms of a study of poly(A) site choice in plants.  In the latter study, it was determined that about 70% of plant genes possess at least two poly(A) sites.

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Fear and polyadenylation

April 17, 2012

No, this post is not about the fear that our favorite subject strikes in the minds of students who are struggling with concepts and principles of gene expression.  Rather, it’s about an interesting story that helps to illustrate (as if this is needed) the relevance of polyadenylation (and specifically poly(A) site choice) to medical science.

Mention has been made on this blog of a correlation between poly(A) site choice and cancer.  Many meta-analyses and high throughput sequencing studies have also noted a related phenomenon – a great deal of alternative polyadenylation that seems to be specific for neural cells and tissues.  One example of this is recalled in a recent paper that suggests a link between an alteration in alternative polyadenylation and aspects of memory and anxiety in mammals (including humans).

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What is a linker histone doing there?

March 3, 2012

By way of introducing this short entry:  as is probably true for most blogs that discuss various and sundry aspects of science, I have tended to focus on reviews or peer-reviewed research papers – “the literature”.  There is, however, a whole lot more to the lab than these finished and polished products.  What I want to do with this entry is a bit different.  Instead of talking about a complete study, I thought I would talk (briefly) about some results from my lab that, for various reasons, never found their way into print.  Ideally, someone will read one of these essays and speak up, telling me just what is going on and how it fits in with other data or models.

The following is one such example, a result that is curious and perplexing.  I chose it because it comes with pretty pictures, and because it is a segue for another essay that I will post in the future.  The data is from a thesis of a student of mine – Kevin Forbes.  The experiment itself is 7-10 years old (I have forgotten just when this study was done), and I made sure that Kevin would be OK with this before I posted anything.

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Eukaryotic mRNA Processing 2011

August 28, 2011

The bi-annual Cold Spring Harbor Laboratory Meeting on Eukaryotic mRNA Processing is one that I try to attend on a regular basis.  The last two meetings (2009 and this year) posed special problems for me, since I am also the driver and mule for Amy’s moving trip to Juniata College.  The two institutions – CSHL and JC – don’t seem to “talk” to each other, and move-in has been coincident with the meeting (basically, 1 day apart, not enough time to drive to PA, return, and fly to NY).  This means that I have ended up driving from Lexington to Cold Spring Harbor for the past two meetings.  Load the car up with a dorm room, drive to Huntingdon PA, unload, and just continue to Long Island.

Well, it turns out that this was a pretty fortuitous choice of travel this year.  The 2011 Eukaryotic mRNA Processing Meeting was, as usual, an exciting and productive one.  But it may well be remembered as much for the bookends of the meeting – the eastern seaboard earthquake that ushered the meeting in on the 23rd, and Hurricane Irene, that necessitated some creative re-scheduling of the last day and a half of the meeting.  Many participants were busier Friday re-scheduling shuttles and flights than listening to presentations.  I was able to leave at the crack of dawn Saturday and beat the storm by about half a day.

The bookends aside, the meeting was excellent (as usual).  I won’t post specifics here (CSHL has rules about commentary and disclosure that I will give a wide berth to).  A few themes do merit mention.  One is that polyadenylation and mRNA 3′ end formation was topical this year.  This is due largely to studies such as I have discussed here and here.  More and more labs have begun to look at alternative polyadenylation in the context of gene regulation and clinical outcomes, and the number of talks and posters that touched on polyadenylation was gratifyingly large.

A second theme was one that has been developing for the better part of a decade.  It has become apparent that the various chapters in the life of an mRNA are not separated, either in time or space.  The connections between the many steps – transcription initiation, elongation, termination, capping, splicing, polyadenylation, transport, translation, etc. – are being revealed in ever more fascinating detail.  This was evident throughout the meeting.

A third theme was technical.  In a nutshell, high-throughput DNA sequencing as applied to RNA has become all the rage.  Lots of people are using variations on the themes I describe here and here to study alternative polyadenylation.  (I hope to be able to discuss additional plant studies in the near future – stay tuned.)  This in addition to other RNA-Seq applications, ChIP-Seq, CLIP-Seq, CRAC (see the brief mention near the bottom of this site), and other acronym-encoded approaches.  (I’m kicking myself for missing an opportunity to come up with my own clever term. Oh well.)  As sequencing becomes more affordable, I think that this trend will continue.

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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.


REM

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.

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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.