This week I finally return to science writing! To start off, I thought I would write a series of posts to describe and critique my recent paper in BMC Evolutionary Biology, “Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes.” (This article is freely available to anyone. You can view a provisional [e.g., not fancy] version of the paper by clicking here. Or you can just take my word for it and read this post.) In this paper, we ask what regions of the cichlid fish genome control the function of genes responsible for vision, and whether any of these regions differ between cichlids that see differently. Today I’ll talk about the background to this study.
Now, there is a lot of background information that goes along with this — especially since this blog is geared towards a general audience. To start with, if you’ve never heard of cichlids, they are a group of beautifully-colored fish found throughout the southern hemisphere. The cichlids we study are found in the three great lakes of East Africa — Lakes Tanganyika, Malawi, and Victoria — though you can also find them at your local pet store. The one cichlid that many people are probably familiar with is the tilapia, which is just a large river-dwelling cichlid. In this study, we primarily focused on two cichlid species, the Nile tilapia (Oreochromis niloticus) and the Zebra cichlid (Metriaclima zebra).
So then what is a gene and which ones control vision? The first part of this question is hard to answer because our view of genes is evolving. It used to be we pictured genes as strings of DNA that encoded some protein (which they do). We also thought that the genome of an organism would be chock full of genes. However, once we actually started to sequence the genomes of complex organisms like humans, we learned that this is not the case. The human genome, for example, is made up of 3 billion base pairs of DNA, but only about 5% of this encodes proteins (the traditional view of a gene). The rest of the genome encodes non-protien-coding genes such as functional RNAs, while other parts encode regulatory sequences, which are small bits of non-coding DNA that proteins bind to in order to help turn genes on and off. Whether these non-coding regions also count as genes or as parts of a gene is under some debate; but even after we count all these, the vast majority of an organisms is still a combination of junk, genomic parasites, and regulatory regions with unknown function.
The second part of my second question — which genes control vision — is easy to answer. The genes that control animal vision are opsins. These genes encode a group of receptor proteins that are turned on, or expressed, in the eye. When light hits these proteins, they absorb it, then send a signal to the retina, which then signals the brain and the visual cortex. This is how humans and other animals see, and all animals that see light use opsins. Humans have three types of opsins used for color vision: SWS, MWS, and LWS, which stand for short-, medium-, and long- wavelength-sensitive. In humans, these opsins preferentially absorb blue, green, and red light, respectively, and all the colors we see are a combination of these three wavelengths. However, cichlids and other fishes have many more opsins. Cichlids have seven opsin genes used for color vision, and the proteins they produce collectively absorb light across the entire visible light spectrum, from ultraviolet to red. But that’s not even the most interesting part. The neat thing is that different cichlid species use different sets of opsins and therefore see the world very differently. For example, some cichlid species use ultraviolet and green opsins, and these fish will see and interpret the world very differently than others that use blue, green, and red opsins. Why different cichlids use alternate opsins not wholly clear, but I’ve shown in other work that at least some of this diversity is explained by what types of food each species feeds on (species that feed on UV-absorbing zooplankton express the ultraviolet-sensitive opsin in their eyes) and the colors of light available in each lake (if there is more blue light present in the environment, then cichlids will use more blue opsin). In this paper, I don’t ask why cichlids use different opsins, but how.
This brings us back to genes and how they work. I mentioned that some of the genome is composed of regulatory DNA. Cis-regulatory DNA is one type of regulatory DNA that is found very near the gene(s) they help turn on or off. Cis-regulatory sequences are relatively short (100 – 500 bp long) and contain binding sites that the regulatory machinery of the nucleus binds to. These nuclear regulatory machines are transcription factors (sometimes call trans-regulatory sequences). The most common type of cis-regulatory sequence is the promoter that is located directly upstream of a gene, but cis-regulatory sequences can also reside in regions further away — sometimes they are even found millions of base pairs away, tucked inside the intron of another gene! Additionally, parts of a gene that are not converted to protein (UTRs, or untranslated regions) can also contain cis-regulatory sequences that are bound by some of those non-coding RNAs I mentioned earlier. This view of the gene and how its function may be changed by cis-, trans-, and other mutations is shown below.
Understanding the genetic basis of gene regulation is a major goal of evolutionary biology, and so our goal for this paper was to identify potential cis-regulatory sequences that control opsin gene use in cichlids. How this is done is a little tricky, since the genetics of gene regulation is a young field. Ultimately, we used a few computational and statistical methods to help us, which I’ll write about next week when I discuss the methods and results of this paper. I like to keep these posts short in order to make them more readable.