The Complex Truth About ‘Junk DNA’
quantamagazine.org
The Complex Truth About ‘Junk DNA’
1–10 of 63 posts
Re: The Complex Truth About ‘Junk DNA’
#2Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,”
Rest of the article: continues to use the term "Junk DNA".
Re: The Complex Truth About ‘Junk DNA’
#3Famously, people with multiple copies of GGGGCC in a particular section of their non-coding DNA are prone to horrible neurodegenerative diseases including ALS (shudder).
Re: The Complex Truth About ‘Junk DNA’
#4Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".
I think more than any other group, programmers can understand the gut reaction of calling code that they don't understand "junk".
Re: The Complex Truth About ‘Junk DNA’
#5Most genetic variants associated with common diseases fall in non-coding DNA areas, previously thought to be junk DNA.
Many of these non-coding areas are actually enhancer elements. These elements produce enhancer RNA, previously thought to be noise, and regulate distant genes thanks to chromosome conformation. Chromosome conformation means DNA folds in complex 3D patterns.
The interplay between chromosome conformation, enhancer RNA, gene expression and disease variants is very complex and interesting [1,2].
I know some startups trying to regulate genes by targeting enhancer elements. The field is very promising, but a big roadblock seems to be to deliver compounds to the right cell type.
Junk DNA was always contentious because there was evidence of conservation in these areas. In other words, evolution was selecting against mutations in some junk DNA regions. My impression is that junk DNA fell quickly out of favor once the ENCODE Project started to publish large scale epigenetics data in the early 2010s.
[1] https://genomebiology.biomedcentral.com/articles/10.1186/s13...
Re: The Complex Truth About ‘Junk DNA’
#6Most genetic variants associated with common diseases fall in non-coding DNA areas, previously thought to be junk DNA. Many of these non-coding areas are actually enhancer elements. These elements produce enhancer RNA, previously thought to be noise, and regulate distant genes thanks to chromosome conformation. Chromosome conformation means DNA folds in complex 3D patterns. The interplay between chromosome conformati…
The fact that enhancers can be transcribed is quite interesting. I’m not sure what’s the function of these transcripts though. It seems like the transcription is terminated prematurely once RNA pol realizes it’s not a functional gene.
Re: The Complex Truth About ‘Junk DNA’
#7Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".
Everyone doing biology professionally already knows the non-coding DNA has function. It’s only logical since we know that resource-intensive mechanisms don’t survive the evolutionary pressure if there’s no benefit for them to exist. So it’d be wasteful to replicate 98% of DNA if it’s not functional. Keep in mind it’s not only replicated, there’s error-correction as well.
Re: The Complex Truth About ‘Junk DNA’
#8Most genetic variants associated with common diseases fall in non-coding DNA areas, previously thought to be junk DNA. Many of these non-coding areas are actually enhancer elements. These elements produce enhancer RNA, previously thought to be noise, and regulate distant genes thanks to chromosome conformation. Chromosome conformation means DNA folds in complex 3D patterns. The interplay between chromosome conformati…
The fact that enhancers can be transcribed is quite interesting. I’m not sure what’s the function of these transcripts though. It seems like the transcription is terminated prematurely once RNA pol realizes it’s not a functional gene.
There's a lot of literature on this, but you are quite right as there are tons of open questions. Some enhancer RNAs are non-functional. Others seem to help stabilizing chromosome contacts. Some do seem to encode secondary structures, so they are probably functional ncRNAs.
Irrespective of this, enhancer RNA transcription is very useful to track active regulatory regions and to perform QTL studies.
Re: The Complex Truth About ‘Junk DNA’
#9Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".
Everyone doing biology professionally already knows the non-coding DNA has function. It’s only logical since we know that resource-intensive mechanisms don’t survive the evolutionary pressure if there’s no benefit for them to exist. So it’d be wasteful to replicate 98% of DNA if it’s not functional. Keep in mind it’s not only replicated, there’s error-correction as well.
it's wasteful to replicate non-functional DNA, yet there are organisms whose genomes are 10X-100X larger than any others (literally ten copies of a genome), and they do just fine (https://en.wikipedia.org/wiki/Paris_japonica). The cost of DNA replication isn't that strong a functional selection afaict.
Re: The Complex Truth About ‘Junk DNA’
#10Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".
Introduction: Introduces term.
Early text: Details evidence that term is misguided.
Late text: Continues to use early term so as to provide a consistent interface to readers. Might use 'scare quotes' if term is particularly egregious but still conserves familiarity of terminology.