Uchida, S. , & Adams, J. C. (2019). Physiological roles of ... · 2 40 15,014 long non-coding RNAs (lncRNAs), and 2,222 miscellaneous ncRNAs, which are ncRNAs 41 that cannot be classified.

Uchida, S., & Adams, J. C. (2019). Physiological roles of non-codingRNAs. AJP - Cell Physiology, 317(1).https://doi.org/10.1152/ajpcell.00114.2019

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1Roles of Non-coding RNAs in Human Diseases 1

[Introductory Editorial for the Theme: Roles of non-coding RNAs in Human Diseases] 2 3 4

Shizuka Uchida1,2 and Josephine C. Adams3 5 1Cardiovascular Innovation Institute, 2Institute of Molecular Cardiology, Department of Medicine, 6

University of Louisville, Louisville, KY 40202, U.S.A. 7 3School of Biochemistry, Faculty of Biomedical Sciences, University of Bristol, Bristol, United 8

Kingdom 9 10

Address for correspondence: S. Uchida, Cardiovascular Innovation Institute, University of 11 Louisville, Louisville KY 40202 (e-mail: [email protected]; [email protected]) 12

13 14 15 MAIN TEXT 16 Research centered on the molecular functions of proteins has uncovered signaling pathways 17 that control pathophysiological processes in cells and tissues. A textbook view of many 18 signaling pathways is that the master regulators are transcription factors that control signaling 19 pathways via gene expression. The latter is influenced by epigenetic marks on genomic DNA; 20 for example, the methylation status of histone proteins. After transcription from genomic DNA, 21 the transcribed RNAs are decoded by ribosomes to produce polypeptides, which are then folded 22 and modified into active proteins. However, over the last 15 years, it has become clear that the 23 relationship of DNA to RNA to protein is not so straightforward. 24 Recent advancements in high-throughput sequencing technologies have uncovered that 25 although the majority of a mammalian genome is transcribed to RNA, only a minor part encodes 26 for functional polypeptides or proteins (1). Traditionally, RNAs that do not encode proteins have 27 been well recognized for their function as housekeeping RNAs: for example, ribosomal RNAs 28 (rRNAs), transfer RNAs (tRNAs) and small nuclear RNAs (snRNAs) have integral roles in 29 translation of RNA into proteins and transcript splicing. Because such housekeeping functions 30 are essential for cellular activities, the non-coding housekeeping RNAs are highly abundant in 31 cells (2) (Fig. 1). For example, in rapidly growing mammalian cells such as HeLa cells, the 32 composition of RNA species is ~80% rRNAs, 15% tRNAs, and 5% all the other RNAs, including 33 protein-coding messenger RNAs (mRNAs) and other non-coding RNAs (ncRNAs) (2). It is now 34 recognized that the other ncRNAs comprise a population of diverse types of ncRNA that control 35 or modify diverse aspects of cell function. According to the latest annotations of human genes at 36 the Ensembl genome database (Assembly: GRCh38.p12), there are 20,418 protein-coding 37 genes; 15,195 pseudogenes, and 22,107 ncRNAs. NcRNAs include 4,871 small ncRNAs [e.g., 38 small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNA), microRNAs (miRNAs), tRNAs]; 39

215,014 long non-coding RNAs (lncRNAs), and 2,222 miscellaneous ncRNAs, which are ncRNAs 40 that cannot be classified. 41 By definition, pseudogenes are sequence-similar to protein-coding genes but lack protein-42 coding potential. LncRNAs are any ncRNAs longer than 200 nucleotides (nt). Although it is a 43 rather popular view that the complexity of an animal (e.g., humans vs. worms) correlates with 44 the number of ncRNAs (3); in reality, the detailed annotation of the genome dictates this view 45 (9). Furthermore, for even the most annotated animal genome, the human genome, the exact 46 number of genes (including ncRNAs) is not currently defined (6). Thus, more detailed 47 annotations of ncRNAs and their functional properties will be needed to fully understand the 48 influence of ncRNAs in cellular activities. With regard to the evolution of ncRNAs, rRNAs can be 49 found in Archae and Bacteria. In eukaryotes other than plants, RNA polymerase (Pol) I 50 synthesizes pre-rRNA 45S and Pol III synthesizes tRNAs, rRNA 5S, and some small nuclear 51 RNAs (snRNAs), while precursors of mRNAs, most of lncRNAs, and a large fraction of small 52 housekeeping RNAs (e.g., miRNAs, snoRNAs, and the majority of snRNAs) are synthesized by 53 Pol II (7). snoRNAs are important small RNAs that are relatively abundant. After synthesis, most 54 of these RNAs are modified (e.g., addition of 5' capping, 3' polyadenylation, and RNA splicing) 55 and localized to their specific subcellular locations to be functional, as in the case of the nuclear-56 enriched lncRNA, Myolinc, which binds to the DNA/RNA-binding protein, Tdp-43 (4). 57 Among the non-housekeeping, regulatory ncRNAs, one of the most well-studied classes is 58 miRNA, for which the mature products are ~22 nt. The primary function of miRNAs is to bind 59 sites in the 3'-untranslated regions (3'-UTR) of protein-coding transcripts, to block their 60 translation. Because one miRNA can target hundreds of genes, miRNAs can be viewed as a 61 machinery that fine-tunes cellular activities at a whole-cell level. Furthermore, due to their 62 stability in circulation (e.g., elevated serum levels of miR-141 in prostate cancer patients (5)), a 63 growing number of miRNAs are under consideration for use as diagnostic biomarkers of various 64 diseases. In addition, the function of a number of understudied classes of ncRNAs are 65 beginning to be understood. Of these ncRNAs, lncRNAs are increasingly being studied. The 66 current data suggest various functions and that dysregulation of lncRNA abundance is also 67 linked to disease – for example, the lncRNA CHRF (8) functions as miRNA sponges in 68 cardiovascular disease. Furthermore, the majority of hits from genome-wide association studies 69 for human disease-associated loci map to non-coding regions, and to lncRNA loci in many 70 cases. 71

In view of the growing evidence for important physiological roles of various forms of 72 ncRNA, the Editors of AJP-Cell Physiology are pleased to start in this issue a thematic series of 73

3Reviews on “Roles of non-coding RNAs in Human Diseases”. The first article by Zhang, Ma and 74 Pearce (10) considers the roles of miRNAs in brain development and the evidence that miRNAs 75 contribute to cerebrovascular pathophysiology. Future reviews in the series will also examine 76 roles of ncRNAs in the physiology and diseases of particular tissues or cell types, or will focus 77 on a specific ncRNA that is emerging in some form as a master-regulator. The Editors thank all 78 the authors for their time and effort in contributing these excellent Reviews. We hope that for 79 readers of AJP-Cell Physiology, these Reviews will provide contexts to consider how ncRNAs 80 may be involved in the cellular and molecular physiology of a multitude of biological processes. 81 Submissions of research articles that investigate the roles of ncRNAs in cell physiology are 82 welcome either as regular research articles or under any of the current Calls for Papers. 83 84 REFERENCES 85 1. Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, 86 Valencia A, and Tress ML. Multiple evidence strands suggest that there may be as few as 87 19,000 human protein-coding genes. Human molecular genetics 23: 5866-5878, 2014. 88 2. Lodish HF. Molecular cell biology. New York: W.H. Freeman, 2000, p. xxxvi, 1084, G-89 1017, I-1036 p. 90 3. Mattick JS. The State of Long Non-Coding RNA Biology. Noncoding RNA 4: 2018. 91 4. Militello G, Hosen MR, Ponomareva Y, Gellert P, Weirick T, John D, Hindi SM, 92 Mamchaoui K, Mouly V, Doring C, Zhang L, Nakamura M, Kumar A, Fukada SI, Dimmeler 93 S, and Uchida S. A novel long non-coding RNA Myolinc regulates myogenesis through TDP-43 94 and Filip1. J Mol Cell Biol 10: 102-117, 2018. 95 5. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, 96 Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen 97 BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, and Tewari M. 98 Circulating microRNAs as stable blood-based markers for cancer detection. Proceedings of the 99 National Academy of Sciences of the United States of America 105: 10513-10518, 2008. 100 6. Salzberg SL. Open questions: How many genes do we have? BMC Biol 16: 94, 2018. 101 7. Vannini A, and Cramer P. Conservation between the RNA polymerase I, II, and III 102 transcription initiation machineries. Molecular cell 45: 439-446, 2012. 103 8. Wang K, Liu F, Zhou LY, Long B, Yuan SM, Wang Y, Liu CY, Sun T, Zhang XJ, and 104 Li PF. The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. 105 Circulation research 114: 1377-1388, 2014. 106 9. Weirick T, Militello G, and Uchida S. Long Non-coding RNAs in Endothelial Biology. 107 Front Physiol 9: 522, 2018. 108 10. Zhang L, Ma Q, and Pearce WJ. MicroRNAs in Brain Development and 109 Cerebrovascular Pathophysiology. Am J Physiol Cell Physiol 2019. 110 111 GRANTS 112 This study was supported in part by National Institutes of Health Grant P30GM127607, V.V. 113 Cooke Foundation (Kentucky, U.S.A.), and the startup funding from the Mansbach Family, the 114 Gheens Foundation, and other generous supporters at the University of Louisville (to S.U.). 115

4 116 DISCLOSURES 117 No conflicts of interest, financial or otherwise, are declared by the authors. 118 119 AUTHOR CONTRIBUTIONS 120 Both authors drafted and revised the manuscript, prepared the figure, and approved the final 121 version. 122 FIGURE LEGEND 123

124

5Fig. 1. Major classes of cellular RNAs. Three types of RNA polymerases (Pol I, II, and III) 125 synthesize different types of RNA species, yielding the indicated composition by weight of RNA 126 transcripts in a typical human cell (lefthand pie chart). The gene number distribution is based on 127 the latest genome annotation provided by the Ensembl genome database (Assembly: 128 GRCh38.p12) (righthand pie chart). piRNAs: Piwi-interacting RNAs; scRNAs: small cytoplasmic 129 RNAs; snoRNA: small nucleolar RNA; and snRNAs: small nuclear RNAs. 130 131