Junk DNA and Genome Evolution

Abstract

Junk DNA (deoxyribonucleic acid) is a remarkably enduring concept considering the difficulty in describing it with a precise undisputed definition and the serious doubts for its usefulness posed by researchers in different biological fields. At the moment, the main value of the junk DNA concept might not depend on what it clearly defines but how it relates with our difficulties in providing satisfying models for the integration of genome organisation, expression and evolution. In a way, junk DNA is not a measure of our knowledge, as much as it reflects our uncertainties. While sanctioning such uncertainties with a specific term might be of very limiting use for areas of research that employ reductionist approaches to mine genomes or find solutions to biomedical and biotechnological problems, the junk DNA concept might still act as enticing fuel for areas that aim to offer an integrative view of biological systems, their diversity and evolutionary history.

Key Concepts

  • Some biological concepts are difficult to describe with simple definitions accepted by all scientific fields.
  • Junk DNA is controversial because it is usually defined in virtue of its uselessness for biological systems well being, and it is unclear which is the best demonstration for the lack of function or effect.
  • Junk DNA might directly descend from protogenomic entities in the RNA world.
  • Junk DNA might facilitate genome evolution by promoting evolutionary capacitance.
  • Junk DNA could be better described as vestiges and facilitators of genome evolution.

Keywords: junk DNA; genome evolution; RNA world; gangen; evolutionary capacitance; heterochromatin

Figure 1. Junk DNA could be better described as vestiges and facilitators of genome evolution. Cartoons symbolising two key aspects of the contribution of junk DNA elements and their earliest ancestors to genome evolution. (a) Within ancient ‘RNA world’ gangens, RNAs with endonuclease and ligase abilities would mediate RNA fragmentation and the formation of multi‐RNA protochromosomes encompassing ‘functional’ domains interleaved with ‘useless’ tracts [see main text and Villarreal and Witzany ; Witzany and Villarreal for further details]. (b) In modern genomes, junk DNA tends to accumulate in chromosome regions with highly compacted chromatin or heterochromatin. Chromosomes mostly formed by junk DNA‐rich heterochromatin, such as Y or W, are known to be very variable in size even for individuals from the same progeny and act as sinks for heterochromatin‐forming elements. In situations characterised by an intensive remodelling of chromatin throughout the genome and limiting amounts of heterochromatin‐forming elements, such as during metazoan fertilisation, individual differences in size for large repositories of junk DNA‐rich heterochromatin will result in a variation in the amount of heterochromatin‐forming elements that are detracted from the limiting pool, and, consequently, a variation in the amount of this material that is left to be deployed in other heterochromatic domains. Thus, chromatin compaction for genes that are located within or next to heterochromatin would vary between individuals, and, because of that, the accessibility of such genes to the transcription machinery and ultimately their expression. The variation in the expression of genes located within or next to heterochromatin indirectly dependent on the junk DNA content of large junk DNA‐rich heterochromatic repositories might contribute to a phenotypic heterogeneity that promotes evolutionary capacitance [see main text and Diaz‐Castillo and Diaz‐Castillo for further details]. In (b), the thickness of lines symbolising heterochromatin is used to convey the variation in chromatin compaction of heterochromatic repositories in chromosome I dependent on the size of the mostly heterochromatic chromosome II. A dashed‐line box is used to highlight the variation in expression for a gene located in chromosome I pericentromeric heterochromatin.
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Villarreal LP (2008) Origin of Group Identity: Viruses, Addiction and Cooperation. New York, NY: Springer Science & Business Media.

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Diaz‐Castillo, Carlos(Oct 2017) Junk DNA and Genome Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0027509]