The central role of RNA in the genetic programming of complex organisms

Notwithstanding lineage-specific variations, the number and type of protein-coding genes remain relatively static across the animal kingdom. By contrast there has been a massive expansion in the extent of genomic non-proteincoding sequences with increasing developmental complexity. These non-coding sequences are, in fact, transcribed in a regulated manner to produce large numbers of large and small non-protein-coding RNAs that control gene expression at many levels including chromatin architecture, post-transcriptional processing and translation. Moreover, many RNAs are edited, especially in the nervous system, which may be the basis of epigenome-environment interactions and the function of the brain.


INTRODUCTION
It appears that the genetic programming of complex organisms has been misunderstood for the past 50 years, because of the assumption -largely true for the unicellular prokaryotes, but apparently not for multicellular eukaryotes -that most genetic information is transacted by proteins.This assumption is based upon the central dogma which holds that 'DNA makes RNA makes protein', implying that RNA functions primarily as an intermediate between a gene and its encoded protein, which in turn are responsible for the core functions of the cell, including regulatory functions.Reciprocally it has been assumed that the vast tracts of non-protein-coding sequences that are present in animal and plant genomes are largely non-functional.However, this assumption may be incorrect (Mattick 1994), and the emerging evidence suggests that these non-coding sequences actually specify a vast and hitherto hidden layer of regulatory information that is transacted by RNAs, in conjunction with generic protein complexes that interact with

INFORMATION SCALING IN COMPLEX ORGANI
The human genome specifies an anatomically co and cognitively advanced organism comprised of cells, with exquisitely precise architecture of its ent muscles, bones, many organs and the brain, w self contains ∼ 10 10 neurons each with an estimate synaptic connections in the neocortex alone (An et al. 2003).Surprisingly the human genome co only ∼20,000 conventional protein-coding genes ( stadt andPonting 2006, Clamp et al. 2007), wh similar in number and largely share orthologou tions with those in nematodes that have only ∼1,0 matic cells.Indeed, not withstanding clade-specifi ations and innovations (such as RNA editing protei below), the core proteome and extent of proteinsequences has not changed greatly since the origin metazoa, despite enormous increases in their de mental and cognitive complexity (Taft et al. 2007 On the other hand, the extent of non-protein-  Kapranov et al. 2007).These ncRNAs generally fall into two size classes: (i) small RNAs that are less than 200 nt, including infrastructural RNAs like tRNAs, rRNAs and small nuclear / spliceosomal RNAs (snRNAs), as well as various types of regulatory RNAs, including micro-RNAs (miRNAs), small interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs) and small nucleolar RNAs (snoRNAs) (Mattick and Makunin 2005); and (ii) long noncoding RNAs (lncRNAs) that can range from a few hundred bases up to well over 100 kilobases in length (Furuno et al. 2006, Pang et al. 2007, Mercer et al. 2009).

REGULATED EXPRESSION OF NONCODING RNA
These lncRNAs show tissue-specific and physiologically-responsive expression (Ravasi et al. 2006) Approximately half of all lncRNAs show highly specific expression patterns in different regions of the brain, and many are trafficked to specific sub-cellular locations (Mercer et al. 2008).Moreover particular ncRNAs are associated with known and novel sub-nuclear domains (Sone et al. 2007, Sunwoo et al. 2009), suggesting a key role for lncRNAs in cell biology that has yet to be explored.While ncRNAs exhibit a wide range of conservation (Pang et al. 2006), this is to be expected given that their sequences are subject to different structure-function constraints (i.e., may be more plastic) than proteins, and that regulatory innovation underpins much if not most of phenotypic variation (Pheasant and Mattick 2007).There is also an underexplored subterranean strata of differentially expressed repeat-derived RNAs (Lunyak et al. 2007, Faulkner et al. 2009), which may also play an important role in developmental regulation (Faulkner andCarninci 2009, Mattick et al. 2010).

RNA REGULATION OF EPIGENETIC PROCESSES
A major function of ncRNAs appears to be the regulation of the epigenetic processes that underpin differentiation and development (Amaral and Mattick 2008), by guiding relatively generic chromatin-modifying complexes to their sites of action (Mattick et al. 2009).Many chromatin-modifying proteins contain RNA binding domains, as indeed do major classes of transcription factors (Shi and Berg 1995, Mattick 2003, 2007, Bernstein and Allis 2005).An increasing number of lncR-NAs have been shown to be associated with chromatinmodifying complexes and different forms of modified histones (Rinn et al. 2007, Dinger et al. 2008b, Nagano et al. 2008, Pandey et al. 2008, Terranova et al. 2008, Zhao et al. 2008, Khalil et al. 2009, Swiezewski et al. 2009).Indeed, ncRNA-directed regulatory circuits underpin most, if not all, complex epigenetic phenom-printing and allelic exclusion, paramutation (see below), and possibly transvection and transinduction (see Mattick andGagen 2001, Mattick 2009b).In addition exons are preferentially associated with nucleosomes in somatic and sperm cells in vertebrates (Nahkuri et al. 2009), indicating that epigenetic regulation acts not just the level of the gene, but at the level of individual exons, which potentially explains the basis of the long-standing mystery of how alternative splicing is regulated, a prediction that has recently gained experimental support (Luco et al. 2010).

MULTIPLE CLASSES OF SMALL RNA
Small RNAs of the miRNA, piRNA and siRNA families play important roles in a wide range of developmental and physiological processes in animals and plants ( Bartel 2004, Jones-Rhoades et al. 2006, Stefani and Slack 2008, Ghildiyal and Zamore 2009), and many are dysregulated in diseases such as cancer (Esquela-Kerscher andSlack 2006, Medina andSlack 2008).Recently, we have discovered a number of new classes of small RNAs, including tiny RNAs associated with transcription initiation sites (tiRNAs) (Taft et al. 2009c) that appear to be related to nucleosome positioning (Taft et al. 2009a), similarly-sized RNAs associated with splice junctions (spliRNAs) (Taft et al. 2010b), and a range of small RNAs derived from snoRNAs (sdRNAs) (Taft et al. 2009b), some of which appear to function as miR-NAs (Ender et al. 2008), indicating an interplay between the snoRNA-and miRNA-mediated regulatory systems (Politz et al. 2009, Taft et al. 2009b).

RNA COMMUNICATION AND PLASTICITY
Finally, it appears that RNA is trafficked between cells (Dinger et al. 2008a).It also appears to be the substrate for the transmission of environmental information into endogenous epigenetic networks, via RNA editing (Mattick 2010).RNA editing occurs via two classes of enzymes, the ADARs (one of which, ADAR3, is brainspecific) that catalyze adenosine deamination to inosine variously on RNA or DNA to catalyze cytosine methylcytosine deamination to uracil or thymine gan et al. 2004, Sawyer et al. 2004, Zhang and 2004, Mikl et al. 2005, Navaratnam and Sarwar RNA editing occurs in most if not all tissues, a to play an important role in development (Bhutan 2010, Sato et al. 2010), and is particularly ac the brain (Bass 2002, Valente and Nishikura 200 triguingly, there is ∼30 times more RNA editi served in human than in mouse, the vast majo which occurs in Alu primate-specific elements nasiadis et al. 2004, Blow et al. 2004, Kim et al. Levanon et al. 2004).The amount of editing h increased during primate evolution associated wi human-specific Alu insertions in genes of neurona tion (Paz-Yaacov et al. 2010).Alu sequences a pear to have been subject to positive selection (La al. 2001), possibly associated with the evolution vanced brain function, which also involves process are similar to those in the immune system (Matti Mehler 2008, Mattick 2010).Finally it appears tha is the mediator of transgenerational epigenetic tance, referred to as 'paramutation' (Chandler 2 process that is also influenced by editing (Nadeau

CONCLUSION
The emerging evidence suggests that, rather than of protein-coding sequences in a desert of jun genomes of humans and other complex org should be viewed as islands of protein-coding seq in a sea of regulation (Mattick 2004, Ovcharenk 2005), most of which is transacted by RNA (Am al. 2008, Mattick 2010).Moreover it appears tha rather than simply being an ephemeral intermedi tween gene and protein, actually comprises the c tational engine of the cell (Mattick 1994, Matti Gagen 2001) and the substrate for epigenome-en ment interactions (Mattick 2010) RNAs grandes e pequenos não-codificadores de proteínas que controlam a expressão de genes em vários níveis, incluindo a arquitetura da cromatina, o processamento pós-transcricional e a tradução.Além disso, muitos RNAs são editados, especialmente no sistema nervoso, o que pode ser a base de interações epigenoma-ambiente e a função do cérebro.
. It is a rema versatile molecule (Leontis and Westhof 2003, Le and Westhof 2006, Cruz and Westhof 2009), w an extended summary of plenary lectures presented at the IRT 2010 (XIX International Round Table on Nucleosides, Nucleotides and Nucleic Acids), Lyon, France, and at the 56 th Brazilian Congress of Genetics, Guarujá, Brazil.The author gratefully acknowledges the support of Australian Research Council Federation Fellowship FF0561986.