Genome complexity: Nature Mag on junk (Introduction)

by David Turell , Wednesday, March 31, 2021, 15:28 (1114 days ago) @ David Turell

This is a review of the human genome project showing junk DNA has in large part disappeared:

https://www.nature.com/articles/d41586-021-00314-6

"Our analysis shows that, between the start of the HGP in 1990 and its completion in 2003 (after the draft was published in 2001), the number of discovered (or ‘annotated’) human genes grew drastically. It levelled out suddenly in the mid-2000s at about 20,000 protein-coding genes (see ‘Twenty years of junk, stars and drugs: Non-coding elements’), far short of the 100,000-strong estimate previously adopted by many in the scientific community.

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"A great debate pre-dated the start of the HGP: was it worth mapping the vast non-coding regions of genome that were called junk DNA, or the dark matter of the genome? Thanks in large part to the HGP, it is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression.

"With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.

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"There are now more than 30,000 papers per year linking SNPs and traits. A large fraction of these associations are in the once-dismissed non-coding regions.

My insertion re' SNPs: "In genetics, a single-nucleotide polymorphism (SNP) is a substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of the population (e.g. 1% or more). For example, at a specific base position in the human genome, the C nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A."

"Cellular function relies on weak and strong links between genetic material and proteins. Mapping out this network now complements the Mendelian perspective. Today, more than 300,000 regulatory network interactions have been charted — proteins binding with non-coding regions or with other proteins.

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"In summary, we think that the HGP is more notable for the new era of genomics it ushered in, than for the protein catalogue itself. As the theory of complex systems shows, an accurate survey of components is necessary — but not sufficient — to understand any system. Complexity arises from the diversity of the interactions between components. After 20 years of research building on the HGP, biologists now have a glimpse of the network structure and dynamics that define life."

Comment: The finding that most all of DNA is coordinated into control systems suggests a high degree of thoughtful design created this code. The disappearance of so-called 'junk' DNA re moves the Darwinian tenet that chance mutations made DNA. But Jerry Moran on his blog still fights for 'junk' as a concept and calls the Nature Mag approach as totally misguided. I view it as desperation.