Witzany, L. P. Villarreal & Guenther

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EDITORIALpublished: 27 March 2018doi: 10.3389/fmicb.2018.00581Frontiers in Microbiology | www.frontiersin.org 1 March 2018 | Volume 9 | Article 581Edited by:David Gilmer,Université de Strasbourg, FranceReviewed by:Cristina Romero-López,Institute of Parasitology andBiomedicine “López-Neyra” (CSIC),SpainRoland Marquet,Architecture et Réactivité de l’ARN,France*Correspondence:Guenther Witzanywitzany@sbg.atSpecialty section:This article was submitted toVirology,a section of the journalFrontiers in MicrobiologyReceived: 11 February 2018Accepted: 14 March 2018Published: 27 March 2018Citation:Villarreal LP and Witzany G (2018)Editorial: Genome Invading RNANetworks. Front. Microbiol. 9:581.doi: 10.3389/fmicb.2018.00581Editorial: Genome Invading RNANetworksLuis P. Villarreal 1 and Guenther Witzany 2*1Center for Virus Research, University of California, Irvine, Irvine, CA, United States, 2 Telos–Philosophische Praxis,Buermoos, AustriaKeywords: RNA Networks, genetic identities, regulatory RNAs, infectious agents, Natural Genetic ContentOperatorsEditorial on the Research TopicGenome Invading RNA NetworksIt has been long accepted that newly acquired biological information is mostly derived fromrandom, error-based’ events (Eigen, 1971). However, the serial nature of acquiring such randomevents makes it very difficult to account for the origin or modification of regulatory networks.There is now abundant empirical evidence establishing the crucial role of non-coding DNA (actingthrough the expression of RNA with its complex biology) to create regulatory control (Mattick,2003; Atkins et al., 2011). Along with the parallel comeback of regulatory RNA in virology, RNA isnow at center stage in how we think about complex organisms (Koonin et al., 2006; Atkins et al.,2011).Regulatory RNAs derive from infectious events and can co-operate, build communities, generatenucleotide sequences de novo and insert/delete themselves into host genetic content (Villarreal,2005; Koonin, 2009). In this sense genome invading RNA networks determine host geneticidentities (self-recognition) throughout all kingdoms including the virosphere (Britten, 2004;Marraffini and Sontheimer, 2010; Villarreal, 2011a). But inclusion of a transmissive viral RNAbiology differs fundamentally from conventional thinking in that it represents a vertical domainof life providing vast amounts of linked information not derived from direct ancestors (Villarreal,2014). Interestingly single RNA stem loops react as physico-chemical entities exclusively, whereaswith the network-cooperation of various RNA stem-loops in a module-like manner biologicalselection emerges (Manrubia and Briones, 2007; Vaidya, 2012; Higgs and Lehman, 2015).Additionally co-operating RNAs outcompete selfish genetic parasites (Hayden and Lehman, 2006;Vaidya et al., 2012).Thus, we can argue, that for DNA based organisms, the introduction of infective collectivesof RNA groups are a central driving force of evolution. Such RNA groups are co-adapted frompersistent infectious agents and now serve as regulatory tools in nearly all cellular processes(Witzany, 2016) as documented in several retrovirus derived mobile genetic elements (Brosius,1999; Villarreal, 2011b; Chuong et al., 2016). Additionally, the resulting productive RNA networksconstantly produce new sequence space (i.e., complex regulation) which not only further serve asadaptation tools for their cell-based host organisms but also provides crucial roles in evolutionarynovelty (Villarreal, 2011b). This RNA productivity results out of the empirical fact that a singleRNA sequence can fold into different and unrelated secondary structures with different functionsin a (environmentally determined) context-depending way (Schultes and Bartel, 2000).Infection derived RNAs serve as the agents of regulatory networks in the cellular transcriptome(Feschotte, 2008; Briones et al., 2009; Koonin, 2009; Villarreal and Witzany, 2010). Withouttranscription from the genetic storage medium of DNA into the living world of such RNA agents,no relevant genetic process in the cellular transcriptome can be initiated (Volff, 2006). RNAs,Villarreal and Witzany Editorial: Genome Invading RNA Networkswith their inherent repeat syntax, format the expression ofcoding sequences and organize the coherent line-up of timelycoordinated steps of replication (Shapiro and von Sternberg,2005). The transport of genetic information to the progeny cells isalso coordinated by these agents (Spadafora, 2017). Furthermore,they are crucial for the cooperation between networks of RNA-stem loops to constitute important nucleoprotein complexessuch as ribosome, spliceosome, and editosome (Witzany, 2011).Therefore, such RNA groups are essential for complex order ofgenome constructions (Witzany, 2014).Additionally of interest is that infectious non-coding RNAsinsert preferentially in non-coding DNA areas, whereas codingDNA usually is not the target (Bushman, 2003; Mitchellet al., 2004; Bartel, 2009). In this perspective the non-codingDNA is the preferred habitat to settle down by infectiousRNAs, e.g., y-chromosome in human genomes (Shapiro, 2002;Villarreal, 2009; Lambowitz and Zimmerly, 2011). This mayindicate that the preferred change in evolutionary processesoccurs in regulatory sections and not in the informationstorage coding for proteins, the main source for “mutations”in previous theoretical concepts of evolution (Villarreal andWitzany, 2013).Frontiers Research Topic Genome Invading RNA Networkshighlights various RNA networks being active in host genomes.Sablok et al. discussed classification, identification androles of tRNA derived smallRNAs across plants and theirpotential involvement in abiotic and biotic stresses. Wang et al.investigated how retrotransposon insertion polymorphisms canimpact human health and disease. Moelling et al. demonstratedthat RNase H-like activities of retroviruses, TEs, and phages,have built up innate and adaptive immune systems throughoutall domains of life. Liu at al. summarize recent advances inunderstanding the roles of miRNAs involved in the plantdefense against viruses and viral counter-defense. Malicki et al.review three retrotransposon classes that might represent adomestication of the selfish elements. Habibi and Salmaniexemplified direct action of RNA networks in shaping thegenome. Pecman et al. compared two different approaches fordetection and discovery of plant viruses and viroids. Nagataet al. found that sequence changes in the RNase H domainand the reverse transcriptase connection domain are responsiblefor subtype classification. Zinad et al. suggest that naturalantisense transcripts interfere with their corresponding sensetranscript to elicit concordant and discordant regulation. Ottesenet al. describe how the abundance of Alu-like sequences maycontribute toward Survival Motor Neuron gene pathogenesis.Ariza-Mateos and Gómez show how RNA viruses mimic keyfactors of the host cell. Spadafora found that spermatozoa actas collectors of somatic information and as delivering vectorsto the next generation. Frías-Lasserre et al. demonstrate howcurrent epigenetic advances on non-coding RNAs has changedthe perspective on evolutionary relevant variations. Scolaroet al. demonstrate that evolutive processes for viruses are nowinterpreted as coordinated phenomenon that leads to global non-random remodeling of the population. Seligmann and Raoultfound that ribosomal RNA stem-loop hairpins resemble thoseformed by viruses and short parasitic repeats infesting bacterialgenomes. Fu et al. provide deep insights into the molecularmechanisms of influenza virus infection.More and more empirical evidence establishes the crucialrole of natural genetic content editors such as viruses andRNA networks to create genetic novelty, complex regulatorycontrol, epigenetics, genetic identity, immunity, inheritancevectors, new sequence space, evolution of complex organisms andevolutionary transitions (Villarreal and Witzany, 2015; Chuonget al., 2016, Spadafora, this issue).Genetic identities of RNA networks such as e.g., group Iintrons, group II introns, viroids, RNA viruses, retrotransposons,LTRs, non-LTRs, SINEs, LINEs, Alus invade and even persistin host genomes (Villarreal, 2009). Also mixed networks ofRNA- and DNA viruses derived parts that integrate into hostgenomes have been found (Stedman, 2015), not forgettingpersistent retroviral infections and the essential roles of reversetranscriptases and related RNase H endonucleases (Moelling andBroecker, 2015).Highly dynamic RNA-Protein networks such as ribosome,editosome and spliceosome together with several context-dependent sequence modificating interactions, such as pseudo-knotting, frame-shifting, loop-kissing, by-passing translationgenerate a large variety of RNA regulatory functions out of agiven DNA content (Cao et al., 2014; Denzler et al., 2014; Peselisand Serganov, 2014; Samatova et al., 2014; Keam and Hutvagner,2015; Atkins et al., 2016).There are reasonable expectations that this new empiricallybased perspective on the evolution of genetic novelty andbiological information will have more explanatory power in thefuture than the “error-replication” narrative of the last century.AUTHOR CONTRIBUTIONSAll authors listed have made a substantial, direct andintellectual contribution to the work, and approved it forpublication.FUNDINGThis research did not receive any specific grant from fundingagencies in the public, commercial, or not-for-profit sectors.REFERENCESAtkins, J. 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This is an open-access article distributedunder the terms of the Creative Commons Attribution License (CC BY). The use,distribution or reproduction in other forums is permitted, provided the originalauthor(s) and the copyright owner are credited and that the original publicationin this journal is cited, in accordance with accepted academic practice. No use,distribution or reproduction is permitted which does not comply with these terms.Frontiers in Microbiology | www.frontiersin.org 3 March 2018 | Volume 9 | Article 581

Editorial: Genome Invading RNA Networks

Villarreal, Luis P,

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Editorial: Genome Invading RNA Networks

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