6 ms·

It's important to be wary of the term 'junk DNA'...just because a segment of a chromosome is noncoding does not mean it has no role in the genome's function. As

by atratus 13y ago

It's important to be wary of the term 'junk DNA'...just because a segment of a chromosome is noncoding does not mean it has no role in the genome's function. Assembly of functional structure ie a Replisome requires formation of elaborate secondary and tertiary 3-D conformations that support the primary replication machinery. This is facilated by topoisomerases, binding proteins, a whole soup of RNAs, and spans of "junk" which allow the necessary conformations. In other cases, the 'junk' can serve to insulate highly conserved genes. "Junk" is a terrible characterization. This is one of those instances where the press/pop media can be a bit behind. Some bchem textbooks from even a few years ago are obsolete. Research into DNA-DNA interaction really has become hotter in only the last few years as we've begun pinning down protein roles. There is a whole layer of interaction between epigenetics, differential RNA splicing, and DNA-DNA feedback that is just mind-boggling.

fabian2k 13y ago
It's very annoying how the media, and sometimes even the university press released, continue to announce that we have finally shown that "junk DNA" is not actually junk DNA. We've known that for decades now, but every time it is announced as if it was a completely new discovery. Of course the extent of non-coding DNA that plays some important role has not been known long, and we surely don't understand it yet completely. But finding that some non-coding DNA has a regulatory function has not been a surprise for decades now.
deleted 13y ago
[deleted]
jonathansizz 13y ago
Describing functional non-coding DNA as junk is obviously incorrect, but the fact remains that most non-coding DNA is indeed non-functional, and therefore junk.
- dekhn 13y ago
  hahahah you're so naive. can you provide some evidence there is any non-functional DNA in the genome? Try hard, now, you're talking to somebody who's studied this for 20+ years.
  - jonathansizz 13y ago
    Despite your patronizing tone, I fear it may be you who is naive. I don't know what field it is that you've been in for the last 20 years, but I suggest you start reading up on genetics and biochemistry, as you've got a lot of catching up to do. In the meantime, here are a few questions for you to think about. You are already aware, of course, that 90% of the human genome is unconserved, that 50% of the genome consists of dead transposons and viruses, and that mice have been generated that are homozygous for megabase-scale deletions with no discernible effects? Perhaps you can come up with some hypotheses that could explain these facts that are consistent with your claim of functionality? You've heard of pseudogenes, right? Why do they look exactly like broken genes? What do they do? Why is there great variability in the sequences of repetitive DNA in many species, including humans? Why do some individuals have many more copies of these tandem repeats than others? Are the extra repeats functional? If so, why does the number of copies change rapidly and stochastically from generation to generation? Do you know anyone who thinks satellite DNA is functional? The links below will help you get started on the basics of genome biology. Good luck. http://www.genomicron.evolverzone.com/2007/04/word-about-junk-dna/ http://www.genomicron.evolverzone.com/2007/04/word-about-jun... http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna....
    - dekhn 13y ago
      Would you mind pointing me to a base in the human genome that you claim is non functional. hg19 coords, please.
    - dekhn 13y ago
      Regarding mice, you are likely referring to Eddy Rubin's paper (I familiar of the work in Eddy's team at Berkeley when I was a postdoc in functional genomics in Steven Brenner's lab). http://www.ncbi.nlm.nih.gov/pubmed/15496924 http://www.ncbi.nlm.nih.gov/pubmed/15496924 "Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals." Note their qualifications. I'm asking for proof. Making a viable mouse that has a lot of deletions is in no way evidence that the regions are nonfunctional. For example, maybe they deleted a conserved element which has cold-shock response potential, but the mouse was raised in a room temperature environment. Many of those "worthless transposons" actually seem to play a role in evolution http://www.sciencedirect.com/science/article/pii/S1369526612001094 http://www.sciencedirect.com/science/article/pii/S1369526612... and others show that even "dead" transposon probably play a role in the evolution of tail exons: http://genomebiology.com/content/11/6/r59 http://genomebiology.com/content/11/6/r59 basically, I know where you're coming from. I used to even believe the dogma. Then I spent some deep time looking at genomes, functional evolution, and biophysics, and came to the conclusion that papers like this: http://www.nature.com/nature/journal/v284/n5757/abs/284604a0.html http://www.nature.com/nature/journal/v284/n5757/abs/284604a0... which influenced an entire generation of scientists, are just wrong. Meaningless speculation in the absence of data! Those of us who have spent a lot of time digging into ENCODE and trying to find the really valuable nuggets are starting to come to the conclusion that vast "deserts" of the genome are in fact filled with rich regulatory elements and other functional (including as-yet uncharacterized elements) elements such as RNA genes that classic mechanisms of DNA-evolution-constraint measurement, like Jukes Cantor, are unable to process.

by atratus 13y ago

fabian2k 13y ago

It's very annoying how the media, and sometimes even the university press released, continue to announce that we have finally shown that "junk DNA" is not actually junk DNA. We've known that for decades now, but every time it is announced as if it was a completely new discovery. Of course the extent of non-coding DNA that plays some important role has not been known long, and we surely don't understand it yet completely. But finding that some non-coding DNA has a regulatory function has not been a surprise for decades now.

deleted 13y ago

[deleted]

jonathansizz 13y ago

Describing functional non-coding DNA as junk is obviously incorrect, but the fact remains that most non-coding DNA is indeed non-functional, and therefore junk.

dekhn 13y ago
hahahah you're so naive. can you provide some evidence there is any non-functional DNA in the genome? Try hard, now, you're talking to somebody who's studied this for 20+ years.
- jonathansizz 13y ago
  Despite your patronizing tone, I fear it may be you who is naive. I don't know what field it is that you've been in for the last 20 years, but I suggest you start reading up on genetics and biochemistry, as you've got a lot of catching up to do. In the meantime, here are a few questions for you to think about. You are already aware, of course, that 90% of the human genome is unconserved, that 50% of the genome consists of dead transposons and viruses, and that mice have been generated that are homozygous for megabase-scale deletions with no discernible effects? Perhaps you can come up with some hypotheses that could explain these facts that are consistent with your claim of functionality? You've heard of pseudogenes, right? Why do they look exactly like broken genes? What do they do? Why is there great variability in the sequences of repetitive DNA in many species, including humans? Why do some individuals have many more copies of these tandem repeats than others? Are the extra repeats functional? If so, why does the number of copies change rapidly and stochastically from generation to generation? Do you know anyone who thinks satellite DNA is functional? The links below will help you get started on the basics of genome biology. Good luck. http://www.genomicron.evolverzone.com/2007/04/word-about-junk-dna/ http://www.genomicron.evolverzone.com/2007/04/word-about-jun... http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna....
  - dekhn 13y ago
    Would you mind pointing me to a base in the human genome that you claim is non functional. hg19 coords, please.
  - dekhn 13y ago
    Regarding mice, you are likely referring to Eddy Rubin's paper (I familiar of the work in Eddy's team at Berkeley when I was a postdoc in functional genomics in Steven Brenner's lab). http://www.ncbi.nlm.nih.gov/pubmed/15496924 http://www.ncbi.nlm.nih.gov/pubmed/15496924 "Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals." Note their qualifications. I'm asking for proof. Making a viable mouse that has a lot of deletions is in no way evidence that the regions are nonfunctional. For example, maybe they deleted a conserved element which has cold-shock response potential, but the mouse was raised in a room temperature environment. Many of those "worthless transposons" actually seem to play a role in evolution http://www.sciencedirect.com/science/article/pii/S1369526612001094 http://www.sciencedirect.com/science/article/pii/S1369526612... and others show that even "dead" transposon probably play a role in the evolution of tail exons: http://genomebiology.com/content/11/6/r59 http://genomebiology.com/content/11/6/r59 basically, I know where you're coming from. I used to even believe the dogma. Then I spent some deep time looking at genomes, functional evolution, and biophysics, and came to the conclusion that papers like this: http://www.nature.com/nature/journal/v284/n5757/abs/284604a0.html http://www.nature.com/nature/journal/v284/n5757/abs/284604a0... which influenced an entire generation of scientists, are just wrong. Meaningless speculation in the absence of data! Those of us who have spent a lot of time digging into ENCODE and trying to find the really valuable nuggets are starting to come to the conclusion that vast "deserts" of the genome are in fact filled with rich regulatory elements and other functional (including as-yet uncharacterized elements) elements such as RNA genes that classic mechanisms of DNA-evolution-constraint measurement, like Jukes Cantor, are unable to process.