Difference between Non-Coding and Junk DNA

[DRKFUTURE]

Hello , I m confused by the plethora of information about Humane Genes online, Some say there is a difference between Non-Coding DNA and Junk DNA, some say there is NOT. I read it in rationalwiki Non-coding DNA" refers to portions of the genome that don't code for proteins, the Rest are Junk. As it says - 

Quote

"Non-coding DNA" refers to portions of the genome that don't code for proteins...Protein-coding and non-coding DNA (known functional DNA) make up about 8.7% of the human genome, and 65% of the rest is known junk. It is assumed that the unknown 26.3% is most likely junk — geneticists and ENCODE project members differ in that ENCODE tends to assume functionality as a null hypothesis (ironically, so do creationists) and real scientists assume non-functionality.

what about Pseudogenes and JUNK RNA, are they Non-Coding or Junk ? Someone pls clarify these thing in layman term.

[Endy0816]

Most of it has some role though not in coding for proteins. Even the DNA that has no functional role at all can still act as a repository of genetic material and buffer against negativly impacting mutations.

Quote

Noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs). Other functions of noncoding DNA include the transcriptional and translational regulation of protein-coding sequences, scaffold attachment regions, origins of DNA replication, centromeres and telomeres.

https://en.m.wikipedia.org/wiki/Non-coding_DNA

Pseudogenes are also noncoding but are related to functional genes.

Imagine if:

condition

1 1 =

start

55 *567 * store

stop

was the functional gene and the pseudogene was:

condition

1 1 =

start

55

stop

*567

start

store

stop

still recognizable but no longer  functions in the way it once did.

 

Edited August 5, 2019 by Endy0816

[DRKFUTURE]

thank u but u dint talk about Junk DNA, I want to knw the difference between Junk DNA and Non-Coding Dna

and what is functional non-coding RNA molecules , it sounds contradicting, how come a non-coding portion(rna) is functional ?As far as I knw, all non-coding portion of a DNA (exons) are removed in RNA Splicing (during Transcription).

Edited August 6, 2019 by DRKFUTURE

[CharonY]

A) the coding generally refers to a protein. Hence a DNA locus coding for a RNA, which in turn does not code a protein is typically called non-coding. However, since their purpose is known, they are generally not termed junk DNA.

B) junk DNA is a bit of a misnomer, as you may have heard, it basically refers to loci with unknown function, but its use is ambivalent and is typically not used to refer to something specific.

[DRKFUTURE]

thnk u, when we say, 'it was originally suggested that over 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA, while 20% of a typical prokaryote genome is noncoding."

DO we mean only 98% of 20,000 Genes we found? or 98% of ALL the DNA (all neucleotides)

[Phi for All]

8 hours ago, CharonY said:

B) junk DNA is a bit of a misnomer, as you may have heard, it basically refers to loci with unknown function, but its use is ambivalent and is typically not used to refer to something specific.

I remember reading somewhere that "junk" was an unfortunate thing to name what we didn't understand. Now we're discovering that, much like macro "junk", there are lots of uses we didn't know about. 

[Prometheus]

 

1 hour ago, Phi for All said:

I remember reading somewhere that "junk" was an unfortunate thing to name what we didn't understand.

Maybe they should have called it Dark DNA. Seems to work in physics. 

[CharonY]

1 hour ago, Phi for All said:

I remember reading somewhere that "junk" was an unfortunate thing to name what we didn't understand. Now we're discovering that, much like macro "junk", there are lots of uses we didn't know about. 

It was more or less based on the (old) assumption that the main purpose of DNA was coding for proteins, and therefore regions devoid of genes (which is mostly found in eukaryotes) would be "junk". This view has changed. However, there are also other definitions of functionality, including for example phenotype-defining. I.e. if a particular region was lost, it may not alter the phenotype in any detectable way. Evolutionary it may still be a benefit, e.g. as a junkyard region for integration of mobile genetic elements. There is is also the question whether structural function (in terms of chromosomal structures) would be included in that definition. Ultimately I am not sure whether that discussion is terribly useful or not, to be honest.

 

9 hours ago, DRKFUTURE said:

DO we mean only 98% of 20,000 Genes we found? or 98% of ALL the DNA (all neucleotides)

Per definitionem genes are coding for proteins. Therefore, they cannot be non-coding.

[Phi for All]

1 hour ago, Prometheus said:

Maybe they should have called it Dark DNA. Seems to work in physics. 

Dark is not just unknown though, it also describes not interacting with the EM spectrum. Junk implies worthlessness.

[StringJunky]

The cell needs codes to operate and regulate the codes that make the proteins:

Quote

What is noncoding DNA?

Only about 1 percent of DNA is made up of protein-coding genes; the other 99 percent is noncoding. Noncoding DNA does not provide instructions for making proteins. Scientists once thought noncoding DNA was “junk,” with no known purpose. However, it is becoming clear that at least some of it is integral to the function of cells, particularly the control of gene activity. For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. Such elements provide sites for specialized proteins (called transcription factors) to attach (bind) and either activate or repress the process by which the information from genes is turned into proteins (transcription). Noncoding DNA contains many types of regulatory elements:

Promoters provide binding sites for the protein machinery that carries out transcription. Promoters are typically found just ahead of the gene on the DNA strand.

Enhancers provide binding sites for proteins that help activate transcription. Enhancers can be found on the DNA strand before or after the gene they control, sometimes far away.

Silencers provide binding sites for proteins that repress transcription. Like enhancers, silencers can be found before or after the gene they control and can be some distance away on the DNA strand.

Insulators provide binding sites for proteins that control transcription in a number of ways. Some prevent enhancers from aiding in transcription (enhancer-blocker insulators). Others prevent structural changes in the DNA that repress gene activity (barrier insulators). Some insulators can function as both an enhancer blocker and a barrier.

https://ghr.nlm.nih.gov/primer/basics/noncodingdna

 

[CharonY]

3 hours ago, Phi for All said:

Dark is not just unknown though, it also describes not interacting with the EM spectrum. Junk implies worthlessness.

It refers to non-functional, to be precise. But even that is difficult, as we can define functionality on several levels, for example functional in terms of coding a protein, functional in regulatory processes, functional in structural aspects, functional in terms of phenotype modulating. Depending on your area of research one may emphasize one over the other.

[Alexander20]

I think StringJunky's post above describes it quite well. I'm very happy to see so many people give their input;  It is quite refreshing.  Non-coding DNA refers to it not coding for a protein product..plain and simple.  This doesn't mean, however, that it doesn't have a purpose..IE it may code for an RNA product.  While the junk dna is, as described by the patrons above, unfortunately named. Much of what we know as 'junk dna' is actually the result of transposable elements. These transposable elements are most certainly not 'junk' and have had a profound impact on the evolution of both prokaryotic and eukaryotic organisms(please don't crucify me).

Edited August 7, 2019 by Alexander20
Drunk

[Phi for All]

18 hours ago, CharonY said:

It refers to non-functional, to be precise. But even that is difficult, as we can define functionality on several levels, for example functional in terms of coding a protein, functional in regulatory processes, functional in structural aspects, functional in terms of phenotype modulating. Depending on your area of research one may emphasize one over the other.

And that was my point about "junk" being an unfortunate term to choose. While it can still be functional, junk is often thought of as worthless garbage.

[CharonY]

1 hour ago, Phi for All said:

And that was my point about "junk" being an unfortunate term to choose.

Not unfortunate when it was coined, especially as it actually had a different connotation. To my knowledge it is commonly attributed to Ohno in the 70s who referred specifically to mutation that render a duplicated gene non-functional, and thus creating a pseudo-gene. These sequences that look like a gene but do not carry functionality due to the mutation were termed junk DNA.

It was only later that the meaning was used broader and in a more diffuse way.

1 hour ago, Phi for All said:

While it can still be functional, junk is often thought of as worthless garbage.

Rarely so, at least no in scientific usage. It is used in more specific context such for example as not playing a functional role in some organism-level capacity (which leaves roles open for sub-cellular functions). Other folks use it in other contexts but essentially it refers to the role of a stretch of DNA that does not encode for a protein or RNA and does not seem to be involved in [insert level of observation].

I.e. it is (generally) not used sweepingly, though there are some (imo rather useless) discussions whether the term should still be used.  And note, for most of the DNA there is still not evidence of functionality