Highlights from #KSDNA, part two

Good morning Americans!

I’m excited to share the highlights from the second half of my trip to Canada for the Keystone Symposia joint meeting on DNA Repair & Genome Maintenance and Replication & Recombination. You can find my my previous posts (covering CRISPRs, Synthetic Lethality, and my highlights from the first two days of the conference) in the aforementioned links. If you’re sick of hearing about this madcap microbiologist’s misadventures in the mountains, I’m sorry, but fret not!

Fret not, but do be cautious!
Fret not, but do be cautious!


This blog will soon be returning to its regularly scheduled programming! I’ve been watching the news coverage surrounding the approval of the arctic apple (a GMO fruit that doesn’t go brown when sliced) and I, of course, can’t wait to add my own two cents (or two-thousand words) into the conversation.

I LOVE apples!
I LOVE apples!

However, that’s a matter for another day. For now, let’s go over some of the exciting things I learned during my final days in Whistler.

Such as: this is the symbol of Canada. I don't know what it's supposed to be, either
Such as: this is the symbol of Canada. I don’t know what it’s supposed to be, either

I will admit that many of the talks I attended in the second half of the conference were a bit outside my wheelhouse. An entire plenary session was devoted to “The Interface Between Chromatin and Genome Maintenance.” Chromatin refers to how DNA is packaged within the nuclei of cells.

DNA packaging is critical to keeping our cells humming along. A single base pair of DNA is tiny, measuring in at just about 0.34 nanometers long. However, each and every human cell contains 6,400,000,000 base-pairs worth of genetic information stored within the two copies of each of our 23 chromosomes. That means that each and every single one of our cells has just about 2 meters of genetic-spaghetti wound up inside its nucleus. Eukaryotes wrap their DNA around proteins called histones, to make structures called nuclesomes, which are themselves arranged into higher order structures called chromatin.

Tightly wound DNA Source: https://www.mun.ca/biology/scarr/Fragile_X_chromosome.html
Tightly wound DNA
Source: https://www.mun.ca/biology/scarr/Fragile_X_chromosome.html

However, any time the cell needs to use a particular stretch of DNA, whether to copy it or turn on a particular gene, the nucleosomes must be rearranged to expose the information of interest. Bacteria (which happen to be my bread and butter) don’t really have histones. There are proteins called SMC (for Structural Maintenance of Chromosomes) in bacteria, that seem to play a role in keeping everything organized, but these proteins certainly aren’t subject to the same complex, multi-level regulation that occurs on histones to shape Eukaryotic chromatin.

Source: Hirano, T. Nature Reviews Mol Cell Biol, 2006
Source: Hirano, T. Nature Reviews Mol Cell Biol, 2006

Even though I was outside my comfort zone during some of the sessions, I learned A LOT. Without further, further ado, here are my highlights from part two!

Took you long enough
Took you long enough

=> Iestyn Whitehouse gave a talk covering chromatin dynamics during lagging strand replication. He has set up an awesome system to specifically sequence nascent lagging strand DNA. After establishing proof of principle in yeast cells, he’s started to investigate replication in the worm C. elegans, as a model for more complex organisms. It turns out that we still don’t know a whole lot about where in the genome replication gets going in higher metazoans, and his system is the perfect tool to address the question.

=> Michelle Debatisse gave a provocative talk about what causes common fragile site instability. Common fragile sites are regions in the genome that are especially prone to breaking and mutating. These regions are linked to all sorts of diseases, such as fragile X syndrome. Fragile sites tend to be located in very long genes, which has led to the model that collisions between replication and transcription cause their instability. Debatisse presented evidence that, although there is an interplay between the two processes at play, premature replication termination in long genes drives common fragile site instability, rather than collisions with the transcription machinery.

=> I learned about two techniques (that are both a few years old at this point) during this session: Repli-seq, which allows scientists to sequence only newly replicated DNA; and Nascent-RNA seq, which lets researchers specifically figure out where and when RNA polymerase is transcribing genome-wide.

=> Dale Wigley‘s presentation about the structure and function of the bacterial double-strand DNA break repair machineries AddAB and RecBCD was mind-expanding. The RecBCD helicase/nuclease machine has been seized by creationists as an example of something so elegant, that it is simply “too complicated to have evolved.” Wigley showed some awesome structural and biochemical data demonstrating precisely how RecBCD DID, in fact, evolve, and how it works on the DNA.

=> Ken Marians is just an amazing biochemist. Full stop. His talk on the protein requirements for nascent strand regression at stalled replication forks was a thorough, methodical, dissection of in vitro DNA dynamics.

Source: Gupta et al., JBC, 2014
Source: Gupta et al., JBC, 2014

=> Johannes Walter gave a very clear talk about the mechanisms of vertebrate replication termination. His experimental system (studying replication of two interlinked plasmids in Xenopus egg extracts) is seriously clever, and the idea that two replisomes might just blow right past each other when forks converge is something I had never before considered.

=> Philipe Pasero found that SAMHD1, which is classically thought to be an anti-HIV restriction factor, plays a role in genome maintenance. Who doesn’t love a protein multi-tasker?


=> Andres Aguilera, the king of R-Loops, gave a talk demonstrating how these RNA-DNA hybrid structures alter chromatin compaction. R-Loops are a big deal in my bacterial world; I had no idea they could also mess with how human chromosomes are packaged.

Source: Aguilera & Garcia-Muse, Mol Cell, 2014
Source: Aguilera & Garcia-Muse, Mol Cell, 2014

=> Joseph Jirincy‘s talk offered an answer for the age old question: How does the mismatch repair machinery know which stand contains the correct base? E. coli bacteria stick a methyl group modification on their DNA; if the replisome makes a mistake in the newly copied DNA, the machine that fixes the error knows which DNA strand is the parent copy (because the new strand won’t be methylated yet). Therefore the proteins use the old strand as a template to correct the improperly inserted base. Eukaryotes (and most bacteria, in fact) don’t do methylate. Jirincy has found that misincorporated ribonucleotides (RNA building blocks) in newly replicated DNA might serve as the signal that tells the mismatch repair machinery which DNA strand is which.

=>Jesper Svejstrup‘s multi-level proteomic, genomic, transcriptomic, DNA-damage specific screen made my head spin with its complexity. His finding that RNA polymerase travels a smaller distance along the lengths of genes after UV exposure is fascinating. He’s already identified a ton of interesting factors with his septuple-omic screen; I’m sure his list of candidate factors is longer than the length of all the DNA inside a human body.

=> The final evening of the conference featured a DJ dance party. We answered the age-old scientific question: how many Ph.D.s does it take to remember how to do the macarena?

Yeahhhhhh….scientists got DOWN

Overall I had a fantastic time in Whistler. I learned more than I ever could have anticipated. I made connections with scientists from all over the country. I laughed, I danced, I even got to sneak off and go skiing!

Although there was so little snow, I almost cried.
Although there was so little snow, I almost cried.

I hope you enjoyed reading my highlights from the conference. Writing them down has certainly helped me to cement the experience in my brain. Keystone Symposia puts on amazing scientific meetings, I hope that I will have the chance to attend many more of these events in the future!

Science and Scenery? Sign me UP!
Science and Scenery? Sign me UP!



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