Much Ado About Methylation!

Many people are surprised to learn that your DNA can express itself differently throughout your lifetime. Genes "respond" to different stressors in your environment by turning themselves on and off, a phenomenon referred to in science as epigenetics. But how exactly does this happen? There are several mechanisms to epigenetics but the most studied by far is what is called DNA methylation. In case you need a refresher, your DNA is made of four nucleotide bases: adenine (A), guanine (G), cytosine (C), thymine (T). DNA methylation occurs when a methyl group (a carbon attached to 3 hydrogens) is attached to a cytosine nucleotide at a promoter region (essentially the "start" location of a particular gene). This diagram demonstrates it pretty well:

The addition of this methyl group makes it difficult for your cells to "read" the gene thus making it effectively turned off. 

Now you are probably thinking, "but Ian, what made you want to talk about this? What does this have to do with marine science? And how on earth do you get your hair to be so perfect in the morning?"

First off, thank you for those incredible questions. The topic came to me whilst I was looking at different sequencing methods and fell into a bit of a rabbit hole reading about "bisulfite sequencing." Essentially, treating DNA with bisulfite (HSO3-) before you sequence it can actually help determine DNA methylation. Normally, un-methylated cytosine when combined with bisulfite gets converted to uracil, one of the nucleotides found in RNA. However, with the addition of that methyl group, the powers of bisulfite become worthless to DNA and it remains the same. 

If bisulfite is superman then that methyl group is its kryptonite

Using this technique researchers can see how the epigenetics of an organism changes before and after certain conditions. Say for instance you wanted to see how a rise in salinity affected the genome of a salmon. After designing the exact specifications for your experiment you would take DNA from one set of salmon under normal salinity and another set with higher salinity. Then, using bisulfite sequencing you can see the differences in methylation between the two groups. Do this enough times and you can start to see a pattern which can help prepare bio-monitoring programs for things like climate change or pollution. 

But whats really exciting about all this is just how much research still has to be done involving epigenetics. Marine invertebrates for instance, are an extremely understudied group when it comes to viewing their methylation patterns. Nudibranchs, a group that is near and dear to my heart, has had no research done on their epigenetics! This is all great news for someone like me who is only just starting their career. Like I have stated before, as biotechnology and sequencing methods have become more advanced, this kind of research is more accessible than ever, opening multitudes of doors for young scientists to fill in our gaps in knowledge.

Matching Deep Sea Larvae to their Adults is Harder than You May Think

Recently this past week while I was creating a reference library for shrimp species in the New England area I came across this paper: "A Mysterious World Revealed: Larval-Adult Matching of Deep-Sea Shrimps from the Gulf of Mexico"

The authors, Dr. Heather Bracken Grissom and Dr. Carlos Varela explain how often times scientists have a habit of incorrectly identifying deep sea species and their larvae as two separate organisms. The example they give in the paper is the giant deep sea shrimp, Cerataspis monstrosus Gray. The University of Hawaii has a great video displaying the adult form of this shrimp set to some pretty snazzy jazz music.

Now after watching that video, what would you expect the early stages of this animal to look like? Were you expecting this?

It's not hard to see how scientists were confused too. To add an extra layer of befuddlement, adult Cerataspis monstrosus live in the abyssal regions of the ocean (around 5,000m) whereas its larvae thrive mostly in the mesopelagic (around 500m).

It turns out this is not uncommon with deep sea organisms. Lots of variability has been observed not only between an organism's larvae and adult stages but their male and female counterparts too. The most famous example of this is when scientists identified three deep sea fish, Whalefish, Bignoses, and Tapetails, only to find out years later that they are all the same fish!

So how do we solve this persistent problem? The answer is by using genetics, bioinformatics, and a lot of statistical inference to match different species to their larval forms. This is by no means a simple procedure, as I am beginning to discover in my own research, but it is exciting!