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31 August 2015

The Enigma of Junk DNA

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One of the outstanding enigmas about our genome is knowing whether all nucleotide sequences that comprise it are functional and what their roles could be. In fact, quite some time ago it was suggested that our genome has a significant fraction that’s devoid of any role, which would make it “junk” DNA. At present, there is an intense debate on this part of the genome, its possible functionality and its possible evolutionary and medical importance.

Junk DNA before genomics

The possibility that a large proportion of human DNA, and eukaryotic genomes in general, could be junk (i.e., has no function) was theoretically proposed in 1972 by a Japanese researcher living in the USA, Susumu Ohno. During the rest of the twentieth century, some of the sequences that form part of that fraction were discovered. As such, the following are considered to be nucleotide sequences devoid of function, among others:

  • Introns (regions within genes initially transcribed into RNA, but are later removed and are not translated into protein).
  • Pseudogenes (duplicated genes that have lost their functionality).
  • Transposons (sequences sometimes related with virus that only carry information for replication and transmission).
  • Satellite DNA (consisting of different size DNA sequences – from a few nucleotide to thousands: micro, mini and macrosatellites- highly repeated that accumulate in certain regions and with no apparent function).
  • DNA spacer between genes.

However, this field of research doesn’t determine what proportion of the genome these non-functional sequences represent in respect to the total, and if there are sequences with functions that are yet to be discovered.

The arrival of the “omics” and the controversial junk DNA

The first draft of the human genome was created in 2001. After obtaining its sequence, it was found that only a small fraction of the human genome, about 2-3%, consists of genes and gene related sequences, thus reducing the initial figure of millions to the subsequent estimation of between 20 and 30,000 genes, with the rest corresponding to the aforementioned “junk”: introns, pseudogenes, transposons, highly repeated DNA, etc.

This draft confirms, for example, that there are millions of transposon related sequences in the human genome, which represents more than one-tenth of the genome. On the other hand, it was revealed that some of the sequences considered as junk DNA may be functional in some tissues or organs and not in others. This is the case of some introns which could therefore be considered as optional or recycled junk.

However, in 2012 the results of a project called ENCODE (ENCyclopedia Of Dna Elements) were published, which argued that 80% of the genome has a “biochemistry” function. Specifically, in first place there are “elements” to give RNAs, some of which (the minority), turn into proteins and others (the majority), are those known as antisense RNA, and in some cases we know their purpose (ribosomal, transfer, interference RNA, etc.) and in other cases we really don’t know what they do.

And secondly (and this is the big news), other DNA “elements” or certain chromatin configurations (the DNA binding plus the histone proteins that cover them) that bind to regulatory protein molecules, therefore influencing the performance of the “normal” genes, those that give proteins. These results led scientists to the conclusion that there is practically no “junk” in the human genome, as well as emphasizing that other “roles” would be found for the rest of the genome.

Those who dispute this conclusion (in addition to the problem of the methods and the statistical analysis), argue that the fact that an “element” of DNA is transcribed into RNA or it binds to a protein, does not necessarily indicate that it has a role. For example, they agree that pseudogenes are transcribed into RNA, but either they don’t produce proteins or the protein they give is not functional.

Finally, in 2015, the results of the project entitled Gtex (Genome-Tissue Expression project) were published, which locates many regions of the human genome that determine changes in the expression of “normal” genes in different tissues and organs of healthy people and which, above all, with its variations from person to person, may be at the root of diseases such as cancer. And then the critics: there are faults in the collection and storage of the samples – most obtained post-mortem from different sources and stored in different conditions – as well as in the analysis methods. In this case, it’s not the genome that’s analyzed, but rather its products, the transcriptomes, RNA and proteins.


After all these investigations, it’s clear that the fraction of the human genome, which can be branded as junk DNA, is not as extensive as initially thought. Nevertheless, there is still much debate as to the possible role of many sequences that are only transcribed into RNA or which, by joining proteins or determining changes in chromatin conformation, may have a regulatory function over the genes that give proteins.

The resolution of this controversy has many connotations, ranging from a philosophical evolutionary point, because if the latest data is confirmed this would mean that there is no waste in our genome, to a medical perspective, since some diseases may be down to abnormalities or variations in the huge genome bag that goes further than giving proteins or even RNA alone. Therefore, we must be attentive to the developments that lie ahead in this field in active research and debate.

Manuel Ruiz Rejón

Granada University, Autonomous University of Madrid


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