Thread: Junk DNA not really "junk"

The human genome contains ca. 3.2 billion base pairs, yet only about 2% codes for genes. The remaining 98% is junk DNA (I prefer the term 'satellite DNA').
However, new evidence shows something interesting: 85.2% of the genome is transcribed to functional RNA molecules:

"The researchers (...) identified thousands of previously unknown, unique RNA sequences. (...) Among the RNA transcribed by the DNA outside of genes, the UCSF researchers identified thousands of previously unknown RNA sequences of a type called lincRNA."

"lincRNA" means "Long, intergenic non-coding RNA"; long (> 200 base pairs) transcripts found in the DNA between genes.
The function of those transcripts is not yet fully understood, but the investigators noticed this:

"Furthermore, these lincRNAs are strongly enriched with intergenic sequences that were previously known to be functional in human traits [SNPs] and diseases [cancer]."

Ergo, not only does it show that DNA is definitely not a few genes surrounded by thousands of non-functional sequences, but it does also demonstrate that there could be a causality between human health, phenotype and our satellite DNA.
I hope that future research will focus on the link between DNA and diseases, in order to find and apply new therapies to cure these diseases.

What do you think?


Sources:
Griffiths, A.J.F. et al. (2012), "Introduction to Genetic Analysis, 10th Edition", Freeman/Macmillan, pp. 312-315
DNA found outside genes plays largely unknown, potentially vital roles: Thousands of previously unknown RNA molecules identified
Hangauer, M.J., Vaughn, I.W., McManus, M.T. (2013), "Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs", PLoS Genetics 9(6), e1003569.

I've always hated the term "junk DNA." We should start classifying everything we don't fully understand as junk! That will surely help scientific pursuit. Sure the "junk" might not be as important, but from what I've heard and read recently it likely plays a larger role than we used to think.

Just because a piece of DNA is transcribed doesn't mean that that piece of DNA has a function. To say that it does requires one to use a very loose and almost pointless definition of function.


Don't forget that a least 60-80% of our genomes consist of defective transposons, retroposons, retroviruses, pseudogenes and the like. Most of our genomes ARE junk. Of the remaining 20-30% some unknown amount if it may be functional. This has been known for nearly 40 years already. Studies like the ones linked are really just looking at some fraction of the 20-30% that is though to have function. Even then, there is still no function that has actually been determined here.


As of now, we still very much live in a world where most of our genomes are thought to be junk.

Originally Posted by Zwirko

Don't forget that a least 60-80% of our genomes consist of defective transposons, retroposons, retroviruses, pseudogenes and the like. Most of our genomes ARE junk. Of the remaining 20-30% some unknown amount if it may be functional.

These percentages are clearly proof of an intelligent designer.
(pun intended)


PS: Thank you for your input; I was not familiar with pseudogenes and carcinogenic retroviruses.

It is even true that some of the DNA in some animals come from other animals. I remember a study reported in New Scientist about gophers having some rattlesnake genes. This happens due to cross infection by retroviruses. If a retrovirus picks up genes from animal species A and then infects animal species B, and passes those genes into the genome of gamete cells, then a whole new generation may arise with 'alien' genes.

It is very likely that those junk DNA's in humans may include genes from other animal species.

Originally Posted by Cogito Ergo Sum

These percentages are clearly proof of an intelligent designer.
(pun intended)

.

I was being rather generous (or conservative) with those percentages, just to be safe. If I was pinned down for more definitive numbers I'd opt for something like:

3% protein coding
90% junk
7% other

Despite the media frenzy and current scientific debate over the ENCODE results, I don't think there is much evidence around to suggest these numbers are too far off; more importantly, there is a great deal to suggest they are pretty accurate.

Update

Two scientists have discovered that essentially all RNA, whether or not it codes for proteins, originates at the same types of locations along the strand of DNA.

Although the function of this 'satellite DNA' is still unknown, this research could contribute to solving certain questions (such as why some diseases cannot be attributed to one particular malfunctioning gene):

""These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'""

(cf. Origins of genomic 'dark matter' discovered)

Alright, space out on the junk DNA part. Compare DNA with a car. What is functional about the car? The engine.. The rest simply helps the engine preform its task as prime functionality. In there, we have simply metal plating, which shapes the vehicle like a car. In there you have structural integrity, you have lights, glass panes, whipers, a battery etc. This all is encoded in DNA as well. However, determining the shape of something, DNA wise is extremely difficult, and thus we don't understand it. We look at DNA for it's function, and thus we only see the engine, the direct code that translates to proteins. Then some other stuff that aid in this functionality. If we could just look at DNA, not as its function, but as it's design, we could see the whole car. But we are only slightly understanding the code to its fullest now.

I wonder what DNA will actually look like if its translated to make it visible to us.

still, is a piece of DNA truly junk if its main function is as a containment area of retroviral injections which prevents the latter from expressing itself ?

Originally Posted by Cogito Ergo Sum

The human genome contains ca. 3.2 billion base pairs, yet only about 2% codes for genes. The remaining 98% is junk DNA (I prefer the term 'satellite DNA').
However, new evidence shows something interesting: 85.2% of the genome is transcribed to functional RNA molecules:

"The researchers (...) identified thousands of previously unknown, unique RNA sequences. (...) Among the RNA transcribed by the DNA outside of genes, the UCSF researchers identified thousands of previously unknown RNA sequences of a type called lincRNA."

"lincRNA" means "Long, intergenic non-coding RNA"; long (> 200 base pairs) transcripts found in the DNA between genes.
The function of those transcripts is not yet fully understood, but the investigators noticed this:

"Furthermore, these lincRNAs are strongly enriched with intergenic sequences that were previously known to be functional in human traits [SNPs] and diseases [cancer]."

Ergo, not only does it show that DNA is definitely not a few genes surrounded by thousands of non-functional sequences, but it does also demonstrate that there could be a causality between human health, phenotype and our satellite DNA.
I hope that future research will focus on the link between DNA and diseases, in order to find and apply new therapies to cure these diseases.

What do you think?


Sources:
Griffiths, A.J.F. et al. (2012), "Introduction to Genetic Analysis, 10th Edition", Freeman/Macmillan, pp. 312-315
DNA found outside genes plays largely unknown, potentially vital roles: Thousands of previously unknown RNA molecules identified
Hangauer, M.J., Vaughn, I.W., McManus, M.T. (2013), "Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs", PLoS Genetics 9(6), e1003569.

Could you please explain it in terms I can comprehend what Junk DNA is? I have never heard the term. Mahalo!

Originally Posted by marnixR

still, is a piece of DNA truly junk if its main function is as a containment area of retroviral injections which prevents the latter from expressing itself ?

To be honest, I have no idea and I am certainly not going to speculate about it.

Originally Posted by babe

Could you please explain it in terms I can comprehend what Junk DNA is? I have never heard the term. Mahalo!

"Junk" DNA is, in essence, DNA that does not seem to code for proteins.
Genes are segments in the DNA sequence that carry information for the production of proteins.
However, when we analyse the entire DNA sequence of an individual, we notice that only 2% of it is made out of genes.
The other 98% seems to be useless (or non-coding), hence the name "junk DNA".

Scientists are now trying to figure out why we have so much "junk" in our genome.

Cheese.

(Will deal with this later- my post went into the wrong thread.)

Originally Posted by Cogito Ergo Sum

Originally Posted by marnixR

still, is a piece of DNA truly junk if its main function is as a containment area of retroviral injections which prevents the latter from expressing itself ?

To be honest, I have no idea and I am certainly not going to speculate about it.

Originally Posted by babe

Could you please explain it in terms I can comprehend what Junk DNA is? I have never heard the term. Mahalo!

"Junk" DNA is, in essence, DNA that does not seem to code for proteins.
Genes are segments in the DNA sequence that carry information for the production of proteins.
However, when we analyse the entire DNA sequence of an individual, we notice that only 2% of it is made out of genes.
The other 98% seems to be useless (or non-coding), hence the name "junk DNA".

Scientists are now trying to figure out why we have some much "junk" in our genome.

Mahalo!! That made perfect sense to me!! I appreciate!

Originally Posted by babe

Mahalo!! That made perfect sense to me!! I appreciate!

You are welcome.
My apologies for the confusion. I sometimes forget to simplify some terms in my thread.

Originally Posted by mat5592

I've always hated the term "junk DNA." We should start classifying everything we don't fully understand as junk! That will surely help scientific pursuit. Sure the "junk" might not be as important, but from what I've heard and read recently it likely plays a larger role than we used to think.

Yes. Too many things we don't understand. So it's junk for now.