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Balancing Copy Number in Ribosomal DNA John H COMMENTARY COMMENTARY Balancing copy number in ribosomal DNA John H. Malone1 5S rRNA. These independently transcribed Institute of Systems Genomics, Department of Molecular and Cell Biology, University of noncoding RNA units must act together to Connecticut, Storrs, CT 06269 form the ribosome (Fig. 1A). It seems challenging to coordinate the production of so many genes but there is Ecologistsrecognizethebalanceofnatureas found that subunits of the array vary together indeed evidence for such coordination. How a complex system that arises from interacting in what they define as concerted copy number is the coordinated expression and production and connected parts; disturbing the balance variation (cCNV). cCNV raises new questions of so many proteins and RNAs to assemble can affect other species in nonlinear and about how CNV can function to restore bal- the ribosome achieved? Common promoter dynamic ways. Like ecosystems, the cell and ance in eukaryotic genomes, especially on the motifs, hormone modulation of translation genome are extensively connected by an assembly and function of the ribosome. rates, duplicate copies and retrotransposition, abundance of molecular interactions. Upset- The eukaryotic ribosome is a macromolec- tandem duplicate arrays, and feedback control ting the molecular balance, through changes ular complex composed of about 80 single loops are used in a variety of organisms to in gene regulation, abnormal copy number copy ribosomal proteins and 4 noncoding synchronize ribosome production (5). There- variants, and changes in cell size can create ribosomal RNAs whose genes are responsible consequences for genome and organismal for translating mRNAs into proteins in all fore, there are diverse strategies to ensure an function (1, 2). In PNAS, Gibbons et al. (3) living cells. The genes that encode these adequate supply of proteins and rRNAs. This advance the idea of genome balance further by RNAs are extensively duplicated and scat- flexibility is illustrated by the rapid changes in identifying a new source of genetic variation tered throughout the genome (4, 5). The non- ribosome protein abundance that occurs in that results in balancing transcriptional sub- coding RNA loci are especially intricate. response to environmental signals, especially units of the ribosome. Using data from human The 45S rDNA locus is transcribed by RNA in response to changes in temperature, me- tabolism, and perturbation from chemicals and mouse, the authors characterized copy polymerase I and spliced to produce the 18S, – number variation (CNV) in tandemly re- 5.8S, and 28S rRNAs. The 5S rDNA locus is (5 7). The ribosome then is a classic model peated ribosomal DNA (rDNA) arrays and transcribed by polymerase III and produces of coordination and illustrates the diversity of ways to achieve balance, which if upset, results in detrimental consequences to the organism. Although rapid responses of the level of A Mammalian Ribosome (80S) Transcriptional Arrays of non-coding RNAs ribosomal proteins are known, it is less clear how responses of ribosomal RNA gene 60S subunit clusters are expressed together. The tandem 28S rRNA duplicated arrays of ribosomal RNA gene clusters account for over 80% of the RNA found in the cell, and these repeated arrays 49 proteins Pol III 5 S 5S5S rRNA are some of the most evolutionarily dynamic 5.8S rRNA regions of eukaryotic genomes, with exten- sive CNV found within and between species Pol I (4, 8). Because these arrays are unlinked, 33 proteins transcribed by different polymerases, and 18 S 5.8 S 28 S 18S rRNA contribute to different parts of the ribosomes, it is interesting to wonder about the role of this extreme variation and how this affects 40S subunit ribosomal assembly. Gibbons et al. (3) address this problem by B 5.8 S 28 S 5 S 5 S using publically available human and mouse 5.8 S 28 S 5.8 S 28 S 5 S short-read DNA-Seq data and develop a com- 5 S putational method to measure copy number 5.8 S 28 S 5.8 S 28 S 5 S 5 S for each of the two independently transcribed 18 S 5.8 S 28 S 5 S arrays: the 45S rDNA locus and the 5S rDNA 5 S 18 S 5.8 S 28 S locus (Fig. 1A).Theauthorsfoundmorethan 18 S 5.8 S 28 S 10-foldvariationinDNAcopynumber, ranging from tens to hundreds of copies, Author contributions: J.H.M. wrote the paper. Fig. 1. The mammalian ribosome is composed of a large subunit (60S) and a small subunit (40S) that are composed The author declares no conflict of interest. of a diverse set of proteins and transcriptional arrays of noncoding RNA loci (A). Gibbons et al. (3) discovered that CNV is coupled among transcriptional units at the DNA level, suggesting a new mechanism to achieve balance of the See companion article on page 2485 in issue 8 of volume 112. ribosome (B). 1Email: [email protected]. www.pnas.org/cgi/doi/10.1073/pnas.1500054112 PNAS | March 3, 2015 | vol. 112 | no. 9 | 2635–2636 Downloaded by guest on September 30, 2021 for both the 45S and 5S rDNA loci and (mean = 75.2 copies in Western Africa and is a new source of genetic variation that significant conservation of this variation be- 74.3 copies in Northern and Western Europe), expands the importance of CNV for un- tween species. This conserved and extensive whereas nearby SNP variation in the genome derstanding genome function, especially CNV reinforces the idea that rDNA loci are easily differentiates these populations. This given the response of cCNV to environ- some of the most hypervariable regions of finding suggests that cCNV variation is un- mental perturbations. It will be important eukaryotic genomes. coupledfromvariationinnearbySNPs. to identify the mechanisms that produce Because the ribosome is composed of two Finally, it has recently been shown that these concerted copy numbers of rDNA main subunits, finding correlated variation in bisphenol A, an industrial chemical used in loci, especially because the loci are un- copy number raises the possibility that this the making of plastics, disrupts expression of linked, are spread throughout the genome, concerted variation produces a balanced stoi- and have little sequence homology. How chiometry to preserveribosomefunction. Gibbons et al. advance copy number is coordinated is not clear Probing this idea of balance further, Gibbons the idea of genome bal- but perhaps some form of nonreplicative et al. (3) compared copy number assignments ance further by identi- nonhomologous DNA repair contributes for each of the loci to determine the consis- to this variation (9). Additionally, what hap- tency. If CNV reflected the stoichiometric fying a new source of pens if cCNV becomes uncoupled? Will this needs of the ribosome, then rDNA loci that genetic variation that disrupt ribosome function? How do these contributetothesamesubunits(the5S,5.8S, copy number variants relate to expression and 28S arrays) (Fig. 1A)shouldhavemore results in balancing levels of the rRNAs? Given the cCNV vari- similarcopieswhencomparedwiththe18S transcriptional subunits ation, presumably there will be a close re- locus, which contributes to a different subunit. of the ribosome. lationship, but measuring the levels of RNA Consistent with this hypothesis, 5S, 5.8S, and will help untangle the function of cCNV. 28S, all members of the large ribosomal sub- genes coding for ribosomal proteins (7). With new genome-engineering technologies unit (60S), had the highest correlations in Given the rapid cCNV in families, it is such as CRISPRs/cas (clustered regularly copy number compared with 18S, which con- interesting to wonder how environmental tributes to the small ribosomal subunit (40S). perturbations like bisphenol A could affect interspaced short palindromic repeats) and These correlation analyses suggest that CNV is the CNV of rDNA. Gibbons et al. (3) TALENs (transcription activator-like effec- coordinated to match stoichiometric demands added bisphenol A to cells and measured tor nucleases) (10), it may be possible to of each ribosomal subunit and may provide the number of copies of rDNA loci relative perturb CNV directly to explore how alter- a way to achieve balance (Fig. 1B). to controls using quantitative PCR. Re- ing copy number among the rDNA sub- The intriguing observation that DNA markably, the number of copies of rDNA units can affect balance of the ribosomal copies are expanding and contracting con- loci was reduced compared with controls, components and the consequences when certedly in a sample of humans and mice and reduced in a way that paralleled cCNV. changed. How does cCNV of rDNA vary raises questions about the speed at which These experiments demonstrate that envi- with the single copy and expressed dupli- these changes occur and how this variation ronmental triggers induce rapid and par- cates of the ribosomal proteins (11)? These may contribute to population variation. On allel loss in copies of 5S and 45S rDNA new questions and the new areas of re- the one hand, Gibbons et al. (3) find that the arrays and may provide mechanistic links search that are inspired by the discovery variation in copy number of rDNA is similar between environmental perturbations and of cCNV will be exciting to address as this between humans and mouse, yet on the other human health and disease. field moves forward, but for now it ap- hand, there is extensive intraspecific varia- The discovery that CNV can vary together, pears that coordination among varying DNA tion. To address how fast this cCNV varia- which is likely to balance the stoichiometry copies is a new way to achieve gene and tion is evolving, Gibbons et al. use pedigree of the parts needed to assemble the ribosome, genome balance. analysis from several families to ask whether cCNV between the 5S and 45S loci covary from parents to offspring. Copy number ex- 1 Birchler JA, Veitia RA (2014) The gene balance hypothesis: Dosage 7 Branco AT, Lemos B (2014) High intake of dietary sugar pansion and contraction of the rDNA arrays effects in plants.
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