The Science of Existence (134) Junk Debunked

Junk Debunked

So much “junk” DNA in our genome. ~ Japanese American geneticist Susumu Ohno in 1972

The academic discipline known as genetics arose from an interest in comprehending heredity. Hence the presumption that the molecular knowledge base of life was merely a currency for inheriting traits. That genetics is a fountain of ongoing cellular activity is a recent idea.

At the beginning of the 20th century Wilhelm Johannsen created the terms phenotype and genotype to correlate traits to genes on a one-to-one correspondence. Research proceeded on that basis, to expanding dismay. Bewildered by the apparent disorder of DNA in humans, geneticists declared much of it useless, as it did not fit their preconceptions.

We were using the idea of “junk” in the genome in the sixties in Cambridge. ~ South African biologist Sydney Brenner

This simpleminded misattribution continued as dogma for decades. Relentless exploration of DNA begat more questions than answers. As complications piled up, the tidy notion of genes unraveled.

Beginning in the 1st decade of the 21st century, DNA sequences previously considered junk – those that do not code for proteins – were found to regulate access and employment of genetic coding.

What was dismissed as junk because it was not understood may well turn out to hold the secrets to human complexity and a guide to the programming of complex systems in general. ~ John Mattick

Only 1.5% of the human genome consists of protein-coding genes. The rest is now called intergenic: DNA sequences between genes. All told, 8.2% of the human genome is presently presumed functionally employed.

Intergenic DNA and RNA play critical roles in regulating genetic expression; the development of cells and organisms, and their intelligence system; enhancing biomolecular performance; and ensuring biological propriety and health. Among other diseases, autism correlates with anomalies in intergenic DNA.

Among other employments, intergenic DNA is read to produce small certain RNA molecules which inhibit protein production by shutting down a ribosome’s protein assembly line. This technique is used when cells are stressed and need to instigate quick responses. RNA molecules can be manufactured much faster than proteins.

Genes are the coding of heritable traits in only the vaguest sense. Such vagary does not serve scientific inquiry.

It makes little sense to have distinctions without meaningful difference: genetic versus intergenic versus epigenetic. All are essential facets of using the artifactual knowledge base by which cells manage their affairs.

Genetics terminology is an instance of historical continuity obscuring understanding, as umbrella terms have been reinterpreted through time to mean different things to different people.

Meanwhile, new terms are piled on to an obsolete paradigm. This jungle of jargon is ill-serving.

The commonly bandied term noncoding is even vaguer than gene, as it encompasses a far more amorphous realm of greater magnitude than protein templates. Further, the notion is inconsonant, as so-called noncoding DNA/RNA functionally codes for regulation rather than production.

In many instances, functionality was simply overlooked. If researchers discovered a sequence that did not correspond to preconception, it was labeled “noncoding” and dismissed. Such disregard was blithe: a product of ignorant assumption of how DNA works. A 2013 survey of protein production uncovered 193 proteins produced by supposed noncoding sequences.

The fact that proteins came from DNA sequences predicted to be noncoding means that we don’t fully understand how cells read DNA, because clearly those sequences do code for proteins. ~ Indian molecular biologist Akhilesh Pandey

In essence, noncoding is merely a replacement for nucleotides previously dismissed as junk; a belated turn of muck into brass, albeit with equally vacuous terminology.

In conventional parlance, long noncoding RNA (lncRNA) differs from small noncoding RNA by the arbitrary distinction of being an identifiable sequence greater than 200 nucleotides. The same goes for microRNA (22 nucleotides), and circular RNA (circRNA), a recently discovered enigma. Naming solely by how something looks under a microscope is hardly helpful, especially when looks bely a plethora of functions among cast members.

The vast majority of trait-associated DNA variations occur in regions of the genome that were once labeled as “junk DNA” because they do not code for proteins. We now know that these regions harbor genetic elements that control where, when, and to what extent specific genes are expressed to make functional RNA and protein products. Therefore, most trait-associated DNA variants are thought to alter not the gene itself, but rather, the regulatory elements that control the process of gene expression. ~ American geneticist Terrence Furey & Indian geneticist Praveen Sethupathy

When cells divide, chromosomes are distributed to daughter cells. Centromeres – specialized chromosome regions – ensure that the chromosomes correctly segregate.

The human DNA for centromeres transcribes to a long noncoding RNA. Instead of producing a protein itself, the RNA product recruits and binds 2 proteins so that a centromere functions properly.

Research into erstwhile “junk” is proving to be an exploration of an incredible web of molecular knowledge with staggering intricacy – the font of life’s unicity.

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. ~ The ENCODE Project Consortium