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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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.


July 12, 2010

The RNA 2010 Meeting has come and gone.  Previously, in a sort of preview of coming attractions, I gave a list (from the conference web site) of the many invited speakers.  What I thought I would do here is toss out some random comments, to give readers a small taste of the meeting.  (One aside – the abstracts are not “open access” and attendees are asked in the abstract book to not cite anything without authors’ consent.  This means that I won’t be very explicit about the individual talks or posters.  However, in a few instances, I will provide links to related papers.)

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The Nobel Prize in Physiology or Medicine 2009

October 5, 2009

The announcement is here.  The award goes to Elizabeth Blackburn, Carol Greider, and Jack Szostak “for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”.  Needless to say, RNA is woven intricately into this subject.

Alternative polyadenylation and cancer

September 26, 2009

This is a follow-up of sorts to a previous essay on the subject of alternative polyadenylation.  In the previous report, I discussed some bioinformatics studies that suggested that the 3′ UTRs of mRNAs change, in bulk, in the course of development in mammals.  The implication of these results is that poly(A) site choice in mammals is regulated, with important functional consequences.

A more recent study by Mayr and Bartel adds to this notion.  These authors studied 3′ UTR length in normal and cancer cells, and found a striking correlation between 3′ UTR length and the expression of oncogenes.  Specifically, higher expression (as is found in cancer cells) is correlated with shorter 3′ UTR.  As 3′ UTR length is determined by the position of the poly(A) site along a transcript, this implicates alternative polyadenylation as one mechanism by which oncogene expression is activated.

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“Where Did All the Flowers Come From?”

September 8, 2009

Carl Zimmer has a good article in the NY Times entitled “Where Did All the Flowers Come From?”   The article summarizes lots of interesting stuff, but I find the speculation regarding the evolution of the endosperm to be particularly though-provoking.  Of course, anytime one mentions genome duplication to me, visions of gene silencing and small RNAs begin dancing in my mind.  A recent article from David Baulcombe’s group merits mention in this context.  This paper describes a developmental study of RNA polymerase IV-derived small interfering RNAs (siRNAs).  The remarkable finding in this paper is the observation that the synthesis of many polIV-derived siRNAs is initated at the onset of the development of the maternal gametophyte, and that these siRNAs are in turn derived from the maternal genome(s) in the endosperm.  This has ramifications for the expression of the different genomes in the endosperm, for genome imprinting, and likely for the evolution of flowers and seed development in plants.

The abstract from the paper:

“Most eukaryotes produce small RNA (sRNA) mediators of gene silencing that bind to Argonaute proteins and guide them, by base pairing, to an RNA target. MicroRNAs (miRNAs) that normally target messenger RNAs for degradation or translational arrest are the best-understood class of sRNAs. However, in Arabidopsis thaliana flowers, miRNAs account for only 5% of the sRNA mass and less than 0.1% of the sequence complexity. The remaining sRNAs form a complex population of more than 100,000 different small interfering RNAs (siRNAs) transcribed from thousands of loci1, 2, 3, 4, 5. The biogenesis of most of the siRNAs in Arabidopsis are dependent on RNA polymerase IV (PolIV), a homologue of DNA-dependent RNA polymerase II2, 3, 6. A subset of these PolIV-dependent (p4)-siRNAs are involved in stress responses, and others are associated with epigenetic modifications to DNA or chromatin; however, the biological role is not known for most of them. Here we show that the predominant phase of p4-siRNA accumulation is initiated in the maternal gametophyte and continues during seed development. Expression of p4-siRNAs in developing endosperm is specifically from maternal chromosomes. Our results provide the first evidence for a link between genomic imprinting and RNA silencing in plants.”

The citation:

Mosher RA, Melynk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC. 2009.  Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460, 283-286 (9 July 2009) | doi:10.1038/nature08084.

Where polyadenylation, siRNAs, and DNA methylation meet

May 14, 2009

It has become more apparent in recent years that the different aspects of gene expression – transcription initiation, transcription elongation, mRNA capping, splicing, and polyadenylation, transport of the mRNA to the cytoplasm, translation, and mRNA quality control – are rather extensively interconnected.  One corollary is that the polyadenylation complex, through various of its subunits, plays roles in various of these other processes.  This has been established for the most parts in mammalian and yeast models, but some recent work in plants is adding new and important variation to this theme.

A most recent of such studies has appeared online on PNAS.  This study, from the lab of Caroline Dean, reveals that the polyadenylation factor subunit FY (a homolog of the yeast protein Pfs2), acting in concert with the flowering regulator FCA, plays a crucial role in chromatin modifications that regulate the expression of the FLC gene.  Interestingly, this effect is not limited to just the FLC gene. Rather, other genes that are silenced by small RNA-mediated DNA methylation also require FY for this silencing.  This provocative finding seems to place FY in some sort of proximity to the small RNA-guided DNA methylation machinery, and may have some relevance to many aspects of transcription and mRNA quality control.

The abstract and citation follows. As always, enjoy. Read the rest of this entry »