June 29, 2013
Junk Sections Of Human DNA Not Really Junk After All

Most DNA in human chromosomes is not transcribed and translated into proteins. So the thinking in some circles has been that this DNA was just basically parasitic junk along for the ride. Since that view never made sense to me I'm happy to report that lots of the "junk" DNA regions get transcribed to make RNA molecules. Given the discoveries in recent years on small pieces of RNA as regulatory molecules it looks like large chunks of the genome code for complex regulatory mechanisms.

A new UC San Francisco study highlights the potential importance of the vast majority of human DNA that lies outside of genes within the cell.

The researchers found that about 85 percent of these stretches of DNA make RNA, a molecule that increasingly is being found to play important roles within cells. They also determined that this RNA-making DNA is more likely than other non-gene DNA regions to be associated with inherited disease risks.

This sort of RNA gets a number of names depending on the size and function and who is writing about it. Watch for non-protein-coding RNA (ncRNA) as a general term or microRNA (miRNA) for shorter signaling RNA pieces.

When will we find out the regulatory roles for most of the signaling RNA? I expect we will benefit from the development of delivery mechanisms to put miRNA into cells to alter gene expression and protein function.

Here is the research paper: The uncharted territory of DNA is transcribed into RNA. This transcribed RNA probably forms complex signaling networks.

Known protein coding gene exons compose less than 3% of the human genome. The remaining 97% is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about the extent of intergenic transcription and whether these intergenic RNAs are functional. Here we directly observed with a large set of RNA-seq data covering a wide array of human tissue types that the majority of the genome is indeed transcribed, corroborating recent observations by the ENCODE project.

One implication of this research: Since more of the DNA is used more of the differences in DNA matter.

Share |      Randall Parker, 2013 June 29 01:52 PM 


Comments
budusan said at June 30, 2013 6:27 PM:

That the majority of the genome is indeed transcribed is entirely expected based on what is known about RNA polymerase activity - at a low noise level it will transcribe all and any DNA. This biochemical activity does not automatically imply function of the resulting very rare transcripts.

This flower has genome that is 50X larger than human:
http://www.asianflora.com/Trilliaceae/Paris-japonica.htm

This flower has genome that is 20X smaller than human:
http://www.ipmdss.dk/cp/graphics/ImageDatabase/ARATH-MAT-700.jpg

Do you really think that the difference between the two flowers necessitates ~1000X difference in the number of functional of elements in the genome?

Ronald Brak said at July 1, 2013 8:26 PM:

If a section of DNA is not conserved and accumulates mutations at random, how could it serve any useful purpose? I don't see how random DNA could be helpful.

bbartlog said at July 4, 2013 5:38 AM:

Budusan: a thousandfold difference in the size of the genome is very interesting, but it suggests some sort of higher level selection at work, even if no function can be imputed to most of the individual elements of the genome(s). We don't looks at a mouse and an elephant and conclude that their sizes are somehow irrelevant to their mode of life, or that they aren't being maintained by selection. Likewise (Ronald), saying 'I don't see how random DNA could be helpful' is pointless... there are many things we don't understand. Yet.

budusan said at July 6, 2013 4:48 PM:

@bbartlog

No, it suggests a LACK of [strong] selection. Which is very consistent with everything else we know about genome evolution and biology responsible for genome enlargement (defective transposons accumulating, mostly). Use your Occam razor to your advantage, my friend!

Ronald Brak said at July 6, 2013 7:01 PM:

bbartlog, let's say you have a computer program taking up a lot of space on your hard drive. You notice that 5% of the files appear to be vital to the running of the program and any change to those files almost always results in the program crashing. But other files that take up 95% of the space seem to be full of random ones and zeros and you can make any changes you like to those files with affecting the operation of the program. How important would you conclude those apparently random files are likely to be?

KenH said at July 10, 2013 6:48 PM:

Ronald, you are close to a good analogy with a hard drive. Just think how hard it is to clean up a hard drive of all old files; early or faulty versions of code or reports, etc. It tends to stay around simply because storage is cheap, and decision making is expensive and requires a higher intelligence and global view. The cell doesn't have much of a global view to help decide what to delete, therefore junk DNA accumulates. In both the cell nucleus, and on your hard drive, the junk data does have some functionality, however in-efficient and intermittent.

Ronald Brak said at July 11, 2013 4:39 PM:

Thanks KenH.

For anyone interested, here are 5 good points on junk DNA by a biochemist: http://sandwalk.blogspot.com.au/2013/07/five-things-you-should-know-if-you-want.html

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