A plea

Novelty in the polyadenylation machinery

Late last fall, I published a short review in WIRES RNA that discussed some curious findings coming out of the growing community of plant scientists whose research touches on mRNA polyadenylation. When we think about the polyadenylation machinery, it is reflexive to consider that the core subunits (the CPSF, CstF, CFIm, and CFIIm subunits) should be essential. Indeed, this is the case in yeast and mammals, as far as one can tell. It is thus very surprising that Arabidopsis is able to grow (sometimes, with almost imperceptible phenotypes) in the absence of several supposedly core subunits. The list of dispensable proteins in plants includes CPSF30, FIP1, CstF77, and CstF64.

What we’ve learned during the blogging hiatus

It’s been seven years or so since I updated this blog. In this post, I hope to summarize a direction my lab has taken in this time. If I am successful, you will see how interesting and exciting this research is, and the new directions we are exploring.

For the better part of 12 years, a main focus of research in my lab has been alternative polyadenylation in plants. I summarized a couple of seminal papers previously – here and here. One of the take-home points of this research was the scope of alternative polyadenylation – how many different poly(A) sites could be used, how usage shifts, and the impacts that shifts in poly(A) site choice have on gene expression. Since 2013, we have published many additional papers on alternative polyadenylation. The three summarized here help to develop a theme that guides current research in my lab.

Well, that was a bit of a break

Hmm… I guess that hiatus was a bit longer than I had anticipated. It’s been more than 7 years, so I guess a few updates are in order. Over the next posts, I will bring this blog up to speed – stuff about my lab, other science-related activities, and odds and ends as befits the history of this blog.

While in Lexington …

… for the recently-started Spring Meet at Keeneland (it really is this pretty), I suggest that you find time to attend the 2013 Naff Symposium at the University of Kentucky. This is an annual event put on by the Dept. of Chemistry and centers on aspects of chemistry and molecular biology. This year’s topic is The Origin of Life, and the line-up of speakers is pretty amazing.

On the 47th day …

47 days into the new year. 5 grant proposals. What to do to interrupt the tedium?

Patenting genes

With a tip of the hat to Tim Sandefur and The Panda’s Thumb, an interesting discussion at SCOTUSBlog on the the case of Association of Molecular Pathology v. Myriad Genetics, one that involves the issue of the patentability of human genes.  Enjoy.

How bad …

… was it?  So bad that my mother called me immediately after the game.  Not to console me, but to gloat.

(What game?  If you have to ask, then …)

You know …

… you’re in a crazy place when the first 11 articles on the Kentucky.com mobile app are about a basketball game. Not a tournament game. Not even a league game. Just a game that a governor decree must be played.

In case you’re wondering, guilty as charged.

Just how widespread is alternative polyadenylation in plants?

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.