The International Journal of Biochemistry & Cell Biology 66 (2015) 20–29 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Contents lists available at ScienceDirect provided by Elsevier - Publisher Connector The International Journal of Biochemistry & Cell Biology jo urnal homepage: www.elsevier.com/locate/biocel Review Functional roles of non-coding Y RNAs 1 ∗ Madzia P. Kowalski , Torsten Krude Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom a r t i c l e i n f o a b s t r a c t Article history: Non-coding RNAs are involved in a multitude of cellular processes but the biochemical function of many Received 18 May 2015 small non-coding RNAs remains unclear. The family of small non-coding Y RNAs is conserved in ver- Received in revised form 3 July 2015 tebrates and related RNAs are present in some prokaryotic species. Y RNAs are also homologous to the Accepted 4 July 2015 newly identified family of non-coding stem-bulge RNAs (sbRNAs) in nematodes, for which potential phys- Available online 6 July 2015 iological functions are only now emerging. Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates and, when bound to the Ro60 protein, they are involved in RNA stability and Keywords: cellular responses to stress in several eukaryotic and prokaryotic species. Additionally, short fragments Non-coding RNA of Y RNAs have recently been identified as abundant components in the blood and tissues of humans Y RNA and other mammals, with potential diagnostic value. While the number of functional roles of Y RNAs is DNA replication RNA stability growing, it is becoming increasingly clear that the conserved structural domains of Y RNAs are essential RNA domains for distinct cellular functions. Here, we review the biochemical functions associated with these struc- tural RNA domains, as well as the functional conservation of Y RNAs in different species. The existing biochemical and structural evidence supports a domain model for these small non-coding RNAs that has direct implications for the modular evolution of functional non-coding RNAs. © 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Contents 1. Introduction and historical overview. .20 2. Y RNAs form RoRNPs that are involved in the regulation of RNA stability and cellular stress responses . 22 3. Y RNAs are essential factors for the initiation of chromosomal DNA replication . 23 4. Y RNA localisation. .25 5. Y RNA loop domain-binding proteins . 25 6. Y RNA-derived small RNAs . 26 7. Conclusions . 27 Acknowledgements. .27 References . 27 1. Introduction and historical overview Small non-coding Y RNAs were first discovered in 1981 as com- ponents of ribonucleoproteins (RNPs) complexed with Ro60 and Abbreviations: sbRNA, stem-bulge RNA; RNP, ribonucleoprotein; PTB, La proteins, autoantigens which are targets of the immune system polypyrimidine tract-binding protein; ZBP1, zipcode binding protein 1; Yrl RNA, in patients suffering from the autoimmune diseases systemic lupus Y RNA-like RNA; snRNA, small nuclear RNA; UV, ultraviolet; PNPase, polynucleotide erythematosus (SLE) and Sjögren’s syndrome (Hendrick et al., 1981; phosphorylase; RYPER, Ro60/Y RNA/PNPase Exoribonuclease RNP; NMR, nuclear magnetic resonance; CD, circular dichroism; RNAi, RNA interference; MO, antisense Lerner et al., 1981). These non-coding RNAs were initially found in morpholino oligonucleotide; MBT, mid-blastula transition; ORC, origin recognition the cytoplasm of mammalian cells (human, mouse and monkey) complex; RoBPI, RoRNP binding protein I; YsRNAs, Y RNA-derived small RNAs. ∗ and were therefore given the prefix ‘Y’, for cytoplasmic Y RNAs, to Corresponding author. distinguish them from nuclear U RNAs (Lerner et al., 1981). E-mail address: [email protected] (T. Krude). 1 There are four non-coding Y RNAs in humans (hY1, hY3, hY4 and Present address: Department of Chemical and Systems Biology, Stanford Uni- versity School of Medicine, Stanford, CA 94305, USA. hY5 RNA; an hY2 RNA was also originally described, but was later http://dx.doi.org/10.1016/j.biocel.2015.07.003 1357-2725/© 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). M.P. Kowalski, T. Krude / The International Journal of Biochemistry & Cell Biology 66 (2015) 20–29 21 Fig. 1. The non-coding human Y RNAs. The nucleotide sequences and secondary structures of hY RNAs are derived from sequence alignment and enzymatic and chemical probing (Teunissen et al., 2000; van Gelder et al., 1994). The conserved structural RNA domains and their associated functions are highlighted for each hY RNA. The size in nucleotides (nt) and molecular weight (kDa) of each RNA is indicated. See main text for references. removed from the list as it was found to be a degradation product and sbRNAs. Therefore, to reconcile this diverse range of functions, of hY1 RNA). Y RNAs are present in all vertebrate species investi- a concept of modular structure and evolution of these RNAs is now gated so far, with between one and four different genes per species becoming apparent (Fig. 3). reflecting gene loss and duplication events during vertebrate evo- Initially, investigations into Y RNA function focussed on the con- lution (Mosig et al., 2007; Perreault et al., 2007). In humans, the served binding sites for Ro60 and La proteins, which are required for four Y RNA genes are clustered together at a single chromosomal Y RNAs to associate with these proteins to form RoRNPs (Chen and locus on chromosome 7q36 (Maraia et al., 1994, 1996). A similar Wolin, 2004). RoRNPs are currently implicated in RNA processing syntenic arrangement of Y RNA genes has been described in other and quality control (Hall et al., 2013; Wolin et al., 2012). The precise vertebrates (Farris et al., 1996; O’Brien et al., 1993). Individual Y cellular function of RoRNPs is not yet clear and furthermore they RNA genes are transcribed by RNA polymerase III from distinct pro- are not essential as deletion mutants of Ro60 are viable. The highly moters (Hendrick et al., 1981; Wolin and Steitz, 1983). Y RNAs are conserved binding sites for Ro60 and La proteins are present in the relatively small at 100 ± 20 nucleotides in size, and fold into char- lower stem and polyuridine tail domains of Y RNAs, respectively acteristic stem-loop secondary structures (Fig. 1). Chemical and (Fig. 1). enzymatic structure probing experiments have revealed that the 5 More recently Y RNAs were shown to be essential factors for and 3 RNA ends hybridise to form predominantly double-stranded the initiation step of chromosomal DNA replication in human cell upper and lower stem domains with an internal loop (Teunissen nuclei (Christov et al., 2006; Krude et al., 2009). Strikingly, the et al., 2000; van Gelder et al., 1994). The nucleotide sequences essential cellular function of Y RNAs in DNA replication is conserved of the lower and upper stems are highly conserved, whereas the in vertebrates and nematodes, since functional inactivation of Y sequences – and hence predicted structures – of the internal loop RNAs in Xenopus laevis and Danio rerio embryos, or of sbRNAs in vary greatly between individual Y RNAs. Caenorhabditis elegans leads to abrogation of DNA replication, cell The existence of Y RNAs is not restricted to vertebrates. The fam- cycle arrest and embryonic lethality (Collart et al., 2011; Kowalski ily of small non-coding stem-bulge RNAs (sbRNAs) in nematodes et al., 2015). In contrast to Ro60 and La binding, this essential func- has recently been shown to be homologous in structure and func- tion resides in the upper stem domain of these RNAs (Gardiner et al., tion to vertebrate Y RNAs (Boria et al., 2010; Kowalski et al., 2015). 2009; Kowalski et al., 2015; Wang et al., 2014). Small non-coding RNAs bearing similarities to vertebrate Y RNAs The loop domain of Y RNAs is diverse in sequence and has been or nematode sbRNAs have also been reported in other eukaryotes, reported to bind several different proteins, including nucleolin, including the insects Anopheles gambiae (Perreault et al., 2007) and polypyrimidine tract-binding protein (PTB) and zipcode binding Bombyx mori (Duarte et al., 2015), and the lancet Branchiostoma protein 1 (ZBP1) (Köhn et al., 2013) (Fig. 1). The roles of the inter- floridae (Mosig et al., 2007). Similar RNAs have also been described actions with these proteins are unclear, but it has been suggested in some prokaryotes, including Deinococcus radiodurans (Chen et al., that they could modulate the subcellular localisation of Ro60 (Sim 2000), Salmonella enterica serovar Typhimurium (Chen et al., 2013), and Wolin, 2011), and also confer specialised cellular functions by Mycobacterium smegmatis and possibly many more (Chen et al., binding preferentially to specific Y RNAs (Hogg and Collins, 2007; 2014). These bacterial RNAs are highly divergent from, and not Langley et al., 2010). Consistent with its wide array of binding homologous with, the four vertebrate Y RNA clades (Perreault et al., proteins, the loop domain has been implicated in modulating the 2007). association of Y RNAs with subnuclear chromatin domains (Zhang Since their discovery in 1981, the Y RNA field has grown consid- et al., 2011). erably, concomitant with the rise in number of independent cellular Finally, small RNA fragments derived from Y RNAs become roles associated with Y RNAs (Fig. 2). Biochemical functions of Y enriched in apoptotic cells, possibly as result of apoptotic RNAs have been mapped to distinct structural domains of the Y degradation processes (Rutjes et al., 1999). However, recent 22 M.P. Kowalski, T. Krude / The International Journal of Biochemistry & Cell Biology 66 (2015) 20–29 Fig.