You may go directly to the tables or first read some of my sales pitch for using "nuon" in genomic terminology.
It is very simple: Nuon can stand for any definable nucleic acid sequence, in DNA or RNA.
The prime reason for finding a short name (retronuon), covering different mobile repetitive elements that are generated by reverse transcription of RNA and integration of the resulting cDNA copy into random positions of the genome was my laziness and reluctance to type "retroelements and retrosequences" prior to the advent of "quickeys" and "macros".
According to the definition of Temin1, retroelements carry an intact or defective open reading frame encoding reverse transcriptase (RT). Retroelements can be further subdivided into retroelements that feature long terminal repeats, also termed retrotransposons or LTR retrotransposons (e.g. proviruses), and retroposons that do not contain LTRs; (e.g. long interspersed repetitive elements, LINEs). In contrast, retrosequences do not encode RT and constitute a highly divergent class. Virtually all RNA types (RNA polymerase I, II, and III transcripts) can serve as templates for retronuons2. Common RNA templates for retronuons are messenger RNAs and small non-messenger RNAs (snmRNAs).
In most of my writings, the above nucleotide sequences have to be addressed as a group. In addition, it occurred to Stephen Jay Gould and myself3, that the definition of a gene has always been murky. Importantly, there are many definable sequences in genomes that have no general names or can only be described in lengthy and, at times, awkward terms. Elements or sequences that spread via retroposition constitute a large segment of this class.
We therefore proposed to use the term nuon (derived from nucleic acid) for any definable nucleic acid sequence (DNA or RNA) and the prefix retro for such nuons that were generated by retroposition3. In order to include the fact that not infrequently retronuons are being co-opted, recruited or exapted4 into novel functions3,5 we included xaptonuon to provide a molecular term for this important evolutionary concept3. Since the majority of newly generated nuons has only the potential to be exapted into a function, in some cases after a considerable time laps, and since most nuons disintegrate in the respective genomes, we filled the gaps by coining potonuons and naptonuons for potentially exaptable nuons or eventually non-aptive nuons3. You may credit Steve for taking the concept of exaptation to the genomic level and blame me for too eagerly filling the gaps leading again to term monsters such as "retroxaptonuons", constructs that would defeat our initial goal of simplification that we achieved with the term nuon. This trap was rightfully critizised by Dan Graur6. Nevertheless, these are important evolutionary concepts that, through invention of appropriate nomenclature, made their way into genomic structure, plasticity and evolution3,7. It is interesting to note that already in 1981, Nei and Tajima responded to the need for a similar definition when they proposed the use of nucleon (a term borrowed from nuclear physics) to describe definable nucleic acid sequences in a more flexible general way8.
Legend to Figure: Not only chromosome segments including entire genes can be amplified within a genome. Repetitive elements, for example, are not considered genes but can be defined as nuons and are generated by efficient amplification, e.g. through retroposition - in which case they may be termed retronuons. The new nuon may have a variety of impacts on a possible neighboring gene including its expression. Each nuon, therefore has the potential to become part of an adjacent gene, including, but not limited to serving as a new acceptor or donor site for splicing, part of a new exon, a transcriptional enhancer or a polyadenylation signal. Because of this potential, a new nuon is always a potonuon. If it indeed is exapted into a new role, it may be termed xaptonuon. If, as is most often the case, the recognizable sequence disappears after a long enough evolutionary time span due to repeated sequence changes leading to attrition, it is considered to be a non-aptation and thus a naptonuon. The latter scenario, however, does not preclude such a neutral drifting sequence being exapted into a new role at any point: An intronic sequence, for example, maybe recruited as novel exon in an existing gene9. Consequently, an additional (vertical) arrow points from potonuon to xaptonuon. Of course, a xaptonuon, in turn, can be duplicated to yield another potonuon.
Recently, Hans-Jörg Rheinberger wrote on page 23210: "The foundering of "The Gene" seems well under way (Burian 1985; Carlson 1991; Falk, 1984, 1986; Fischer, 1995). Recently, Jürgen Brosius and Stephen Jay Gould have come up with a new terminology. They propose to abandon the gene concept altogether and to call any segment of DNA that has a recognizable structure and/or function (such as a coding segment, a repetitive element, a regulatory element) nuon. By duplication, amplification , recombination, retroposition, and the like, nuons can give rise to potonuons, that is, entities potentially recruitable as new nuons. These in turn have either the chance of being transformed into naptonuons, that is, dissipate their nonadaptive former information without acquiring new ones, or else into xaptonuons, that is elements exapted to a new function (Brosius and Gould, 1992, 1993). As tempting as this evolutionary genome terminology may be, its operationality remains to be tested. One of its drawbacks may be that it remains completely restricted to the level of DNA adaptation."
Just for the record: We did not suggest abandoning the "gene concept altogether" and we included any nucleic acid, including RNA, in our concept.
Rheinberger10 concluded with an important reference to the "fuzziness theory" as the gene concept itself is fuzzy. In my opinion, our additional terminology makes it less fuzzy, albeit at the cost of minimally adding five (nuon, xaptonuon, potonuon, naptonuon, retronuon) novel terms. In the end, even dozens of terms will not enable us to account for the fuzziness of biological systems. L.A. Zadeh11 has introduced "Fuzzyness theory" and its impact for biological systems including Medicine has been summarized recently by K. Sadegh-Zadeh12.
Analysis of genomes reveals the tremendous impact of retronuons. This is supported not only by the fact ~42% of the entire human genome comprises discernible retronuons, but also in the propensity of retronuons to generate new genes, new coding domains of genes, and regulatory elements including those that can modulate spatial and temporal expression patterns. This recruitment of novel domains and generation of alternate expression patterns is a major driving force of evolution.
We see examples of vertebrate
Here we go: link to tables