Dark DNA and Junk DNA The Story Behind It

Dark matter is one of the biggest mysteries of astronomy today. There’s tons of evidence that it’s there, but try as we might we haven’t been able to find it.In biology there’s a similar problem: darkDNA.When scientists were exploring the sequenced genomes of certain birds and rodents they noticed something odd.A sequenced genome means everything is laid bare, and yet certain DNA sequences were missing, which was weird because these DNA sequences were very important. They controlled the production of leptin in the birds or the secretion of insulin in the rodents, genes that the scientists knew had to to be there, otherwise they’d have some mighty  obese birds and dead rodents on their hands.What’s more, the scientists studying the rodents found the products of the missing DNA sequences in their cells, so they deduced that the genes weren’t missing, but were somehow hidden.They dubbed these elusive sequences “darkDNA.”Sounds spooky, but the reality is this darkDNA may be more of a blind spot in our DNA sequencing technology than anything else.

A closer look at the rodent’s genome found a heavily mutated section with abnormally high amounts of guanine and cytosine, two of DNA’s four base molecules, called G andC for short.It turns out GC rich sequences are difficult to detect, so the researchers missed this mutated pocket of DNA at first.This dark DNA raises questions about how quicklymutations occur, and what genes we may have missed when we sequenced other genomes like our own which is crazy to think that there could bemore DNA in us than we realized, especially when you consider that we only know what about1 to 2% of the stuff we have found. Does those sections code proteins that have somefunction.The other 98%-ish doesn’t make anything and so we don’t know why it’s there.

This vast amount of genetic code has also been referred to as DNA’s “dark matter.”Apparently biologists love the dark matteranalogy, only the kind we’re talking aboutnow is the opposite of the first example.Instead of knowing what a gene does but not finding it, we’ve found a lot of genes but have noDNA idea what they do.Slowly though we’re chipping away at that riddle too.It appears that a lot of this non-coding DNAis still helpful for regulating gene expression,making sure the right cells have the right hardware, like haemoglobin in blood cell precursors and ion channels in neurons.Some of these sequences are almost identical across different species like humans, mice and chickens.Considering we’ve been evolving separately for up to 200 million years, researchers concluded that these sequences must somehow be vitalto our survival.

When researchers deleted four of these genes in mice, they found abnormalities in the mice’s brains, and wondered if mutations in these overlooked non-coding sections of DNA could be responsible for brain diseases like Alzheimer’s. So there is a lot of DNA to parse through and there could be even more we just haven’t found because of limitations in our sequencing techniques.Our genome is still a pretty dark and mysterious place, and more research is needed.Researchers believe that the rodents’ hotspots of DNA mutation could be evidence ofan undiscovered and rapid mechanism of evolution.There are known cases of rapid evolution.
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What is junk dna??

In genetics, the term junk DNA refers to regions of DNA that are noncoding.
DNA contains instructions (coding) that are used to create proteins in the cell. However, the amount of DNA contained inside each cell is vast and not all of the genetic sequences present within a DNA molecule actually code for a protein.
Some of this noncoding DNA is used to produce non-coding RNA components such as transfer RNA, regulatory RNA and ribosomal RNA. However, other DNA regions are not transcribed into proteins, nor are they used to produce RNA molecules and their function is unknown.

The proportion of coding versus noncoding DNA varies significantly between species. In the human genome for example, almost all (98%) of the DNA is noncoding, while in bacteria, only 2% of the genetic material does not code for anything.
History of junk DNA

The term “junk DNA” was first used in the 1960s, but was formalized by Susumu Ohno in 1972. Ohno noticed that the amount of mutation occurring as a result of deleterious mutations set a limit for the amount of functional loci that could be expected when a normal mutation rate was considered. In a Nature review published in the 1980, Leslie Orgel and Francis Crick stated that junk DNA “had little specificity and conveys little or no selective advantage to the organism."
However, over the years, researchers have found evidence to suggest that junk DNA may provide some form of functional activity. Some lines of evidence suggest that fragments of what were originally non-functional DNA have undergone the process of exaptation throughout evolution. Exaptation refers to the acquisition of a function through means other than natural selection.
In 2012, a research program called the ENCODE project concluded that around three quarters of the noncoding DNA in the human genome did undergo transcription and that almost 50% of the genome was available to the proteins involved in genetic regulation such as transcription factors.
However, these findings have been criticized by other scientists who claim that the accessibility of these genomic segments to transcription factors does not mean they necessarily have any biochemical function or that transcription of the segments is in any way advantageous in terms of evolution.

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