How Much Junk Is in Your DNA Trunk?

once a year or so a study makes the rounds that supposedly ends the idea of junk DNA like we thought most of our genome was garbage but this time we're sure that it's not see it the human genome is 3.2 billion base pairs long and contains around 20,000 genes stretches of DNA that code for protein but those genes only make up about one to two percent of our DNA the other 99% of our genome is non-coding and the question of whether it's useless or not has been hotly debated by biologists since the term junk DNA was coined in the 1960s so is there really a bunch of DNA that doesn't do much of anything or does it all do something and we just haven't figured out what it seems like our genomes shouldn't be mostly junk it takes energy to copy and maintain large amounts of DNA so it seems like we should get rid of any extra baggage and well it's pretty easy for biologists to say that coding DNA does something it's tricky to make the call about different types of non-coding DNA protein coding DNA has a clear and elegant function a stretch of DNA is transcribed to RNA and a cell's nucleus and then translated into a protein proteins do things that you can pretty easily study like helping with chemical reactions are building a cellular structure and humans are made up of thousands of types of cells which each need different kinds and amounts of proteins to do their jobs so every cell needs a way of handing out instructions for how much to make of what stuff enter transcription factors proteins that increase or decrease the chance that a gene will be transcribed into RNA they can be switched on in response to all kinds of things like chemical signals from outside the cell or a certain stage in the organisms development and this is where a couple important types of non-coding DNA come into play with a clear purpose transcription factors bind to DNA but not directly to genes instead they bind to stretches of DNA that don't code for anything but have a direct effect on genes for instance promoters are right in front of genes there where the machinery that transcribes RNA actually comes together and gets to work when a transcription factor binds to a promoter it helps everything get going now naming all of the different kinds of non-coding DNA and what they do would be a little much but let's talk about a couple you might have heard of before like there are introns gaps in coding regions that seem kind of like junk but actually a cell can cut them out to mix and match segments of coding regions and create variants of a protein from a single gene there are also bits of non-coding DNA that get transcribed into RNA that never gets translated into a protein collectively called non-coding RNAs the structures that directly assemble proteins called ribosomes are partially made up of non-coding rnas and transfer RNAs shuttle around the building blocks of proteins some others like micro RNAs and long non-coding rnas act more like transcription factors they change the expression of a certain gene or region of the genome in indirect ways so molecular biologists are interested in studying things like all the nitty-gritty functions of transcription factor binding sites and non-coding RNAs and by some definitions any DNA that binds to a transcription factor or gets transcribed into RNA is considered functional which seems like a victory for the anti junk way of thinking this idea peaked in 2012 thanks to the publication of a lot of research by an international consortium known as encode it's short for encyclopedia of DNA elements they made a remarkable claim that 80% of the human genome is functional in some way encode used a variety of molecular biology techniques to support this idea most of them had something to do with whether a transcription factor binds to a given piece of DNA for example chips seek is a way to isolate segments of DNA where a particular transcription factor binds which scientists can then sequence the idea behind encode is really cool it was meant to help anyone who wanted to study specific stretches of DNA like a database of what binds there and what non-coding RNAs are produced but there was immediate push back against that 80% of the human genome is functional idea it wasn't that encodes research was bad this was a huge international group of reputable scientists their definition of functional was just way too generous as even some of the authors admit it's like great you found places where transcription factors stick to DNA but some regions of DNA can be kind of sticky certain proteins might tend to bind there purely by chance and that doesn't necessarily mean anything is happening there other than stickiness that's only one criticism of many but you get the idea saying 80% of our genome is functional is probably too generous now different fields of biology work with different scientific tools molecular biologists research very small biochemical reactions and the like as their name suggests meanwhile evolutionary biologists are studying genome function through a broader lens like trying to figure out why different organisms have vastly different genome sizes for instance onions and African lungfish have way more DNA than humans do meanwhile tougher fish seem to have weirdly little no one's complaining that humans are better than onions and that they somehow deserve to have more DNA it's just that being a human and being an onion are two very different things and it shouldn't take five times more DNA to be an onion even if they are very tasty and have all those layers like ogres the simplest answer to this puzzle is that a lot of DNA just isn't doing anything it's junk even though maintaining extra DNA might be a little more energetically costly the process of natural selection might not stop it from piling up unless it seriously affects survival and turns out having extra DNA could also maybe help in some cases consider pseudogenes which led to the coining of the term junk DNA pseudo genes are what happened when a gene gets duplicated initially both copies probably work if one of them picks up a beneficial mutation tada you got a brand new gene thanks evolution but if one picks up a detrimental mutation the duplicated gene stops working while the original chugs on normally the messed up version doesn't get pruned from the genome though it hangs around as a non-functional bit of DNA that still mostly looks like a gene hence pseudo gene a junky left over our genome is also littered with viral sequences from old infections loss there are transposons which encode proteins that let that segment of DNA cut itself out of the genome and squeeze in somewhere else that's all they seem to do they just jump around because they listen to House of Pain too much every now and then a paper assigns a function to some viral gene or transposon but those seem to be in the vast minority and there are a handful of other types of junk that don't seem to do anything for us it's hard to estimate how much of the genome is non-functional because these elements are pretty repetitive repetition tends to throw off our sequencing methods because those methods rely on looking at a bunch of copies of the genome at once it's like throwing 600 copies of Hamlet into a blender the unique parts like alas poor Yorick they're fairly easy to spot but how many times does Shakespeare use the word the' if you just get a the you don't know where to put it overall a lot of the data in support of junk DNA comes from population genetics which involves a lot of math big one paper published in 2017 in the journal genome biology and evolution instead of looking at where transcription factors bind their definition of functional hinged on whether a DNA sequence could be acted on by natural selection in a positive or negative way most mutations that are subject to natural selection are bad because they break some cellular system and make survival less likely the study's author estimated their rates that harmful mutations build up in humans compared to our rate of reproduction and effective population size that's a statistical term that refers to how much of the population is finding mates and making babies basically natural selection can only eliminate harmful mutations as fast as a species can breed or they would slowly die out but mutations in junky regions wouldn't have bad consequences so they would stick around this paper tried to calculate what it would take to maintain a human genome that's 80 percent functional even using a conservative estimate of mutation rate it concluded that every human couple would have to have 15 children 13 of which would survive and have children of their own which is super unrealistic an earlier paper published by UK researchers in 2014 in PLoS genetics used a similar definition of functional they compared the rates of change of mammalian genomes to one another genes come and go across evolutionary time but by comparing related groups side-by-side researchers can figure out the most important regions a subject natural selection they found that protein coding genes and certain non-coding elements were pretty stable for example promoters were less stable than coding regions but mostly stayed put but other non-coding stretches like transposons weren't really preserved across species and therefore they might not do much interestingly both of these studies independently came up with similar estimates for how much of the genome is functional the 2017 studies suggested the absolute upper limit for how much of the genome has a function is around 25% but favored a more conservative figure of 10 to 15% in the 2014 study landed at 8.2 percent that's obviously way less than encodes sweeping 80 percent claim and those estimates still leave room for functional non-coding elements on top of the coding stuff so we still don't have a clear answer for what's junk DNA and what's not because how scientists define functional varies a lot and we're still trying to understand everything our genomes can do there's a lot of complexity and those 3.2 billion base pairs and we'd be foolish to think we know every trick but it's also foolish to think that evolution is so elegant that there's barely any room for messiness evolution has no end goal and no sense of aesthetics it's a whole lot of probability so sometimes stuff piles up like DNA that doesn't do anything in the end we may have to meet in the middle ground to reconcile both of those ideas and of course keep learning thank you for watching this episode of scishow I thought it was really good I liked it if you want to learn more about DNA and really all kinds of science you can go to youtube.com/scishow to subscribe there is also I think a little button right under this video

Channel: SciShow

Views: 214,660

Rating: 4.947083 out of 5

Keywords: SciShow, science, Hank, Green, education, learn, genetics, dna, rna, transcription factors, junk dna, natural selection, mutations, energy, protein

Id: b5YIdxeMGJY

Length: 10min 56sec (656 seconds)

Published: Wed Sep 19 2018