Thanks, S…… I’ve ALWAYS been fascinated with the idea of the “genome as a community.” When scientists knock out one gene — in one cell-type (or globally) — this loss is somehow “sensed.” Then the genome “sets up a committee,” and they “quickly decide which gene (or genes) will compensate and take over that function (or functions), because their buddy has disappeared.” In the case of these selfish genetic elements, these guys represent an “independent group of invaders”; they do their own thing, and they are not part of the “deciding committee.”
How does the cell (or genome) “detect” the missing gene, or DNA segment? And why are these “invaders” not detected as foreign material? These are very fascinating mysteries that I hope will be solved one day.
DwN
Nebert, Daniel (nebertdw)
Tue 3/19, 1:43 PM
This [attached] review is an excellent overview by Andrew G Clark (population and Drosophila geneticist, at Cornell University since 2oo2, head of the Graduate Computation Biology Field, and member of a working group for the National Human Genome Research Institute) of the topic “selfish genetic elements” (historically also referred to as ‘selfish genes’, ‘ultra-selfish genes’, ‘selfish DNA’, ‘parasitic DNA’ & ‘genomic outlaws’). The empirical study of selfish genetic elements (which had begun in the 1920s) benefited greatly from emergence of the so-called “gene’s-eye view of evolution” in the 1960s and 1970s. In contrast with Darwin’s original theory of evolution by natural selection that — focused on individual organisms — the gene’s-eye view considers the gene to be the central unit of selection in evolution. The “gene’s-eye view” was a synthesis of the population genetics models of the modern synthesis, in particular, the work of R A Fisher, and social evolution models of Bill Hamilton. The view was popularized by George Williams’ and Richard Dawkins‘ books.
In 1980, two high profile papers (published back-to-back in Nature by Leslie Orgel & Francis Crick, and Ford Doolittle & Carmen Sapienza, respectively) brought the study of selfish genetic elements to the center of biological debate. The papers took their starting point in the contemporary debate of the so-called C-value paradox (i.e. lack of correlation between genome size and perceived complexity of a species). Both papers attempted to counter the prevailing view of the time that “presence of differential amounts of non-coding DNA and transposable elements is best explained from the perspective of individual fitness.”
Selfish genetic elements have now been described in most groups of organisms, and they demonstrate a remarkable diversity in the ways by which they promote their own transmission. Though long dismissed as genetic curiosities, with little relevance for evolution, they are now recognized to affect a wide swath of biological processes — ranging from genome size and architecture to speciation.
This outstanding review is divided into sections (Conceptual developments; Current views; The logic of selfish genetic elements; Rule 1 (The spread of selfish genetic elements requires sex and outbreeding); Rule 2 (The presence of selfish genetic elements is often revealed in hybrids); Examples of selfish genetic elements; Homing endonucleases; Transposable elements; B chromosomes [i.e. chromosomes not required for viability or fertility of the organism, but exist in addition to the normal (A) set]; Selfish mitochondria; Genomic imprinting; Greenbeard genes (genes having the ability to recognize copies of itself in other individuals, and then making its ‘carrier act’ preferentially toward such individuals); Consequences of selfish genetic elements to the host; Species extinction (perhaps one of the clearest ways to see that the process of natural selection does not always have organismal fitness as the sole driver is when selfish genetic elements have their way without restriction; in such cases, selfish elements can, in principle, result in species extinction); Speciation; Genome size variation (the C-value — animals vary 7,000 fold and land plants some 2,400-fold — has a long history in biology); Applications of selfish genetic elements in agriculture and biotechnology; Cytoplasmic male sterility in plant breeding; “PiggyBac” vectors (while many transposable elements seem to do no good for the host, some transposable elements have been “tamed” by molecular biologists so that the elements can be made to insert and excise at the will of the scientist); CRISPR gene drive and homing endonuclease systems; Mathematical theory of selfish genetic elements; Segregation distorters; Gene drive systems; and Transposable elements.
Selfish genetic elements have gone from “being seen as genetic oddities with little significance” — to “being considered as major players in evolution”. We now know that their presence, and co-evolution with suppressors, can affect a range of features at the genome, phenotype, and population levels. Whereas the influx of whole-genome data has done much to bring this shift about, particularly for the study of transposable elements, developments in mathematical modeling has also played a key role. Adaptation of CRISPR technologies to engineer gene drive systems for population control has added a new rapidly advancing applied dimension to the study of selfish genetic elements. [You might get the perception that this is one of my favorite topics.] 🙂
DwN
PLoS Genet Nov 2o18; 14: e1007700