Junk

[billvon]

I have been encountering a lot of discussion about hidden codons in junk DNA

1) No such thing as "junk DNA." Most of it does something. A more accurate term is "noncoding DNA" which means it is not actively used to transcribe mRNA for further use in protein synthesis within the cell.

2) The codons aren't "hidden." Any valid sequence of three nucleotides that can code for an amino acid is a codon. The DNA around those codons - and other determinants within the cell, including epigenetic factors, DNA methylation and histone modification - determine how it's used.

3) Noncoding DNA plays a role in apoptosis (through telomere erosion) and cell divison (through centromere creation.) And even noncoding DNA creates things like tRNA and mRNA.

4) Evolution will result in deactivation of some traits via noncoding rather than DNA mutation. Those are technically noncoding, but are remnants that can be 'turned back on' on occasion. Usually this reactivation is a bad thing for the organism. Example here would be dolphins who are born with hind limbs - makes it harder to swim.

 

[Wizard of Whatever]

1) No such thing as "junk DNA." Most of it does something. A more accurate term is "noncoding DNA" which means it is not actively used to transcribe mRNA for further use in protein synthesis within the cell.

It is called junk DNA in many articles I have read.

2) The codons aren't "hidden." Any valid sequence of three nucleotides that can code for an amino acid is a codon. The DNA around those codons - and other determinants within the cell, including epigenetic factors, DNA methylation and histone modification - determine how it's used.

They are hidden in the sense that there are no delimiters before and after the sequences as there are in regular DNA.

3) Noncoding DNA plays a role in apoptosis (through telomere erosion) and cell divison (through centromere creation.) And even noncoding DNA creates things like tRNA and mRNA.

If it creates RNA it is no longer non-coding.

4) Evolution will result in deactivation of some traits via noncoding rather than DNA mutation. Those are technically noncoding, but are remnants that can be 'turned back on' on occasion. Usually this reactivation is a bad thing for the organism. Example here would be dolphins who are born with hind limbs - makes it harder to swim.

 

[billvon]

They are hidden in the sense that there are no delimiters before and after the sequences as there are in regular DNA.

There are very often delimiters - specifically start and stop codons - in junk DNA. They are not read for a variety of reasons, including misalignment and proximity to coding segments. They are also sometimes read but used to create tRNA instead, thus making them non-coding but readable.

If it creates RNA it is no longer non-coding.

That's a terminology thing. If it does not code for a protein, it is noncoding. Therefore even sequences that result in generation of RNA are noncoding if that RNA does not produce a protein.

 

[Wizard of Whatever]

There are very often delimiters - specifically start and stop codons - in junk DNA. They are not read for a variety of reasons, including misalignment and proximity to coding segments. They are also sometimes read but used to create tRNA instead, thus making them non-coding but readable.



That's a terminology thing. If it does not code for a protein, it is noncoding. Therefore even sequences that result in generation of RNA are noncoding if that RNA does not produce a protein.

OK. This is different than I have read elsewhere.

 

[Pinball1970]

It is called junk DNA in many articles I have read.

It's just a bit of a sexy title, like "the god particle."
The term will probably become redundant.