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Zhou S, Lizarazo S, Mouli L, Chorghade S, Cheng R, Rajendra KC, Kalsotra A, Van Bortle K. Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601767. [PMID: 39005375 PMCID: PMC11245037 DOI: 10.1101/2024.07.02.601767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
RNA polymerase III (Pol III) activity in cancer is linked to the production of small noncoding (nc)RNAs that are otherwise silent in most tissues. snaR-A (small NF90-associated RNA isoform A) - a hominid-specific ncRNA shown to enhance cell proliferation, migration, and invasion - is a cancer-emergent Pol III product that remains largely uncharacterized despite promoting growth phenotypes. Here, we applied a combination of genomic and biochemical approaches to study the biogenesis and subsequent protein interactions of snaR-A and to better understand its role as a putative driver of cancer progression. By profiling the chromatin landscapes across a multitude of primary tumor types, we show that predicted snaR-A upregulation is broadly linked with unfavorable outcomes among cancer patients. At the molecular level, we unexpectedly discover widespread interactions between snaR-A and mRNA splicing factors, including SF3B2 - a core component of the U2 small nuclear ribonucleoprotein (snRNP). We find that SF3B2 levels are sensitive to high snaR-A abundance and that depletion of snaR-A alone is sufficient to decrease intron retention levels across subpopulations of mRNA enriched for U2 snRNP occupancy. snaR-A sensitive genes are characterized by high GC content, close spatial proximity to nuclear bodies concentrated in pre-mRNA splicing factors, and functional enrichment for proteins involved in deacetylation and autophagy. We highlight examples of splicing misregulation and increased protein levels following snaR-A depletion for a wide-ranging set of factors, suggesting snaR-A-driven splicing defects may have far-reaching effects that re-shape the cellular proteome. These findings clarify the molecular activities and consequences of snaR-A in cancer, and altogether establish a novel mechanism through which Pol III overactivity may promote tumorigenesis.
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Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Leela Mouli
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sandip Chorghade
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruiying Cheng
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - K C Rajendra
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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2
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Zhou S, Van Bortle K. The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1782. [PMID: 36754845 PMCID: PMC10498592 DOI: 10.1002/wrna.1782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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3
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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4
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Smalheiser NR. The RNA-centred view of the synapse: non-coding RNAs and synaptic plasticity. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0504. [PMID: 25135965 PMCID: PMC4142025 DOI: 10.1098/rstb.2013.0504] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
If mRNAs were the only RNAs made by a neuron, there would be a simple mapping of mRNAs to proteins. However, microRNAs and other non-coding RNAs (ncRNAs; endo-siRNAs, piRNAs, BC1, BC200, antisense and long ncRNAs, repeat-related transcripts, etc.) regulate mRNAs via effects on protein translation as well as transcriptional and epigenetic mechanisms. Not only are genes ON or OFF, but their ability to be translated can be turned ON or OFF at the level of synapses, supporting an enormous increase in information capacity. Here, I review evidence that ncRNAs are expressed pervasively within dendrites in mammalian brain; that some are activity-dependent and highly enriched near synapses; and that synaptic ncRNAs participate in plasticity responses including learning and memory. Ultimately, ncRNAs can be viewed as the post-it notes of the neuron. They have no literal meaning of their own, but derive their functions from where (and to what) they are stuck. This may explain, in part, why ncRNAs differ so dramatically from protein-coding genes, both in terms of the usual indicators of functionality and in terms of evolutionary constraints. ncRNAs do not appear to be direct mediators of synaptic transmission in the manner of neurotransmitters or receptors, yet they orchestrate synaptic plasticity—and may drive species-specific changes in cognition.
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Affiliation(s)
- Neil R Smalheiser
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA
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5
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Conti A, Carnevali D, Bollati V, Fustinoni S, Pellegrini M, Dieci G. Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data. Nucleic Acids Res 2014; 43:817-35. [PMID: 25550429 PMCID: PMC4333407 DOI: 10.1093/nar/gku1361] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Of the ∼1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼1300 Alu loci corresponding to detectable transcripts, with ∼120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5′-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.
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Affiliation(s)
- Anastasia Conti
- Department of Life Sciences, University of Parma, 43124 Parma, Italy Department of Clinical and Experimental Medicine, University of Parma, 43126 Parma, Italy
| | - Davide Carnevali
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, University of Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via S. Barnaba, 8-20122 Milano, Italy
| | - Silvia Fustinoni
- Department of Clinical Sciences and Community Health, University of Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via S. Barnaba, 8-20122 Milano, Italy
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-7239, USA
| | - Giorgio Dieci
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
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6
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Parrott AM, Mathews MB. The evolution and consequences of snaR family transposition in primates. Mob Genet Elements 2014; 1:291-295. [PMID: 22545241 PMCID: PMC3337139 DOI: 10.4161/mge.18478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The small NF90 associated RNA (snaR) family of small noncoding RNAs (ncRNA) appears to have evolved from retrotransposon ancestors at or soon after pivotal stages in primate evolution. snaRs are thought to be derived from a FLAM C-like (free left Alu monomer) element through multiple short insertion/deletion (indel) and nucleotide (nt) substitution events. Tracing snaR’s complex evolutionary history through primate genomes led to the recent discovery of two novel retrotransposons: the Alu/snaR related (ASR) and catarrhine ancestor of snaR (CAS) elements. ASR elements are present in the genomes of Simiiformes, CAS elements are present in Old World Monkeys and apes, and snaRs are restricted to the African Great Apes (Homininae, including human, gorilla, chimpanzee and bonobo). Unlike their ancestors, snaRs have disseminated by multiple rounds of segmental duplication of a larger encompassing element. This process has produced large tandem gene arrays in humans and possibly precipitated the accelerated evolution of snaR. Furthermore, snaR segmental duplication created a new form of chorionic gonadotropin β subunit (CGβ) gene, recently classified as Type II CGβ, which has altered mRNA tissue expression and can generate a novel short peptide.
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Affiliation(s)
- Andrew M Parrott
- Department of Biochemistry and Molecular Biology; New Jersey Medical School; University of Medicine and Dentistry of New Jersey; Newark, NJ USA
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7
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Castella S, Bernard R, Corno M, Fradin A, Larcher JC. Ilf3 and NF90 functions in RNA biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:243-56. [PMID: 25327818 DOI: 10.1002/wrna.1270] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Abstract
Double-stranded RNA-binding proteins (DRBPs) are known to regulate many processes of RNA metabolism due, among others, to the presence of double-stranded RNA (dsRNA)-binding motifs (dsRBMs). Among these DRBPs, Interleukin enhancer-binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by mutually exclusive and alternative splicings of the Ilf3 gene. They share common N-terminal and central sequences but display specific C-terminal regions. They present a large heterogeneity generated by several post-transcriptional and post-translational modifications involved in their subcellular localization and biological functions. While Ilf3 and NF90 were first identified as activators of gene expression, they are also implicated in cellular processes unrelated to RNA metabolism such as regulation of the cell cycle or of enzymatic activites. The implication of Ilf3 and NF90 in RNA biology will be discussed with a focus on eukaryote transcription and translation regulation, on viral replication and translation as well as on noncoding RNA field.
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Affiliation(s)
- Sandrine Castella
- Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, Sorbonne Universités, UPMC Univ Paris 06, Paris, France; Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, CNRS, UMR 7622, Paris, France
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8
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Matylla-Kulinska K, Tafer H, Weiss A, Schroeder R. Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:591-600. [PMID: 25045147 PMCID: PMC4233971 DOI: 10.1002/wrna.1243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/15/2014] [Accepted: 04/22/2014] [Indexed: 12/19/2022]
Abstract
The human genome is scattered with repetitive sequences, and the ENCODE project revealed that 60–70% of the genomic DNA is transcribed into RNA. As a consequence, the human transcriptome contains a large portion of repeat-derived RNAs (repRNAs). Here, we present a hypothesis for the evolution of novel functional repeat-derived RNAs from non-coding RNAs (ncRNAs) by retrotransposition. Upon amplification, the ncRNAs can diversify in sequence and subsequently evolve new activities, which can result in novel functions. Non-coding transcripts derived from highly repetitive regions can therefore serve as a reservoir for the evolution of novel functional RNAs. We base our hypothetical model on observations reported for short interspersed nuclear elements derived from 7SL RNA and tRNAs, α satellites derived from snoRNAs and SL RNAs derived from U1 small nuclear RNA. Furthermore, we present novel putative human repeat-derived ncRNAs obtained by the comparison of the Dfam and Rfam databases, as well as several examples in other species. We hypothesize that novel functional ncRNAs can derive also from other repetitive regions and propose Genomic SELEX as a tool for their identification.
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Affiliation(s)
- Katarzyna Matylla-Kulinska
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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9
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Lee H, Kim C, Ku JL, Kim W, Yoon SK, Kuh HJ, Lee JH, Nam SW, Lee EK. A long non-coding RNA snaR contributes to 5-fluorouracil resistance in human colon cancer cells. Mol Cells 2014; 37:540-6. [PMID: 25078450 PMCID: PMC4132306 DOI: 10.14348/molcells.2014.0151] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 12/11/2022] Open
Abstract
Several types of genetic and epigenetic regulation have been implicated in the development of drug resistance, one significant challenge for cancer therapy. Although changes in the expression of non-coding RNA are also responsible for drug resistance, the specific identities and roles of them remain to be elucidated. Long non-coding RNAs (lncRNAs) are a type of ncRNA (> 200 nt) that influence the regulation of gene expression in various ways. In this study, we aimed to identify differentially expressed lncRNAs in 5-fluorouracil-resistant colon cancer cells. Using two pairs of 5-FU-resistant cells derived from the human colon cancer cell lines SNU-C4 and SNU-C5, we analyzed the expression of 90 lncRNAs by qPCR-based profiling and found that 19 and 23 lncRNAs were differentially expressed in SNU-C4R and SNU-C5R cells, respectively. We confirmed that snaR and BACE1AS were downregulated in resistant cells. To further investigate the effects of snaR on cell growth, cell viability and cell cycle were analyzed after transfection of siRNAs targeting snaR. Down-regulation of snaR decreased cell death after 5-FU treatment, which indicates that snaR loss decreases in vitro sensitivity to 5-FU. Our results provide an important insight into the involvement of lncRNAs in 5-FU resistance in colon cancer cells.
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Affiliation(s)
- Heejin Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Chongtae Kim
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Ja-Lok Ku
- Cancer Research Institute and Cancer Research Center, Seoul National University, Seoul 110-744, Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Sungjoo Kim Yoon
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
- Department of Biomedical Science, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Hyo-Jeong Kuh
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
- Department of Biomedical Science, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
| | - Suk Woo Nam
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
- Department of Pathology, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
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10
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Oliver KR, Greene WK. Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA 2011; 2:8. [PMID: 21627776 PMCID: PMC3123540 DOI: 10.1186/1759-8753-2-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/31/2011] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are increasingly being recognized as powerful facilitators of evolution. We propose the TE-Thrust hypothesis to encompass TE-facilitated processes by which genomes self-engineer coding, regulatory, karyotypic or other genetic changes. Although TEs are occasionally harmful to some individuals, genomic dynamism caused by TEs can be very beneficial to lineages. This can result in differential survival and differential fecundity of lineages. Lineages with an abundant and suitable repertoire of TEs have enhanced evolutionary potential and, if all else is equal, tend to be fecund, resulting in species-rich adaptive radiations, and/or they tend to undergo major evolutionary transitions. Many other mechanisms of genomic change are also important in evolution, and whether the evolutionary potential of TE-Thrust is realized is heavily dependent on environmental and ecological factors. The large contribution of TEs to evolutionary innovation is particularly well documented in the primate lineage. In this paper, we review numerous cases of beneficial TE-caused modifications to the genomes of higher primates, which strongly support our TE-Thrust hypothesis.
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Affiliation(s)
- Keith R Oliver
- School of Biological Sciences and Biotechnology, Faculty of Science and Engineering, Murdoch University, Perth W. A. 6150, Australia
| | - Wayne K Greene
- School of Veterinary and Biomedical Sciences, Faculty of Health Sciences, Murdoch University, Perth W. A. 6150, Australia
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11
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Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer 2011; 10:38. [PMID: 21489289 PMCID: PMC3098824 DOI: 10.1186/1476-4598-10-38] [Citation(s) in RCA: 1314] [Impact Index Per Article: 101.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/13/2011] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as new players in the cancer paradigm demonstrating potential roles in both oncogenic and tumor suppressive pathways. These novel genes are frequently aberrantly expressed in a variety of human cancers, however the biological functions of the vast majority remain unknown. Recently, evidence has begun to accumulate describing the molecular mechanisms by which these RNA species function, providing insight into the functional roles they may play in tumorigenesis. In this review, we highlight the emerging functional role of lncRNAs in human cancer.
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Affiliation(s)
- Ewan A Gibb
- British Columbia Cancer Agency Research Centre, Vancouver, Canada.
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12
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Nagirnaja L, Rull K, Uusküla L, Hallast P, Grigorova M, Laan M. Genomics and genetics of gonadotropin beta-subunit genes: Unique FSHB and duplicated LHB/CGB loci. Mol Cell Endocrinol 2010; 329:4-16. [PMID: 20488225 PMCID: PMC2954307 DOI: 10.1016/j.mce.2010.04.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 04/13/2010] [Accepted: 04/26/2010] [Indexed: 01/28/2023]
Abstract
The follicle stimulating hormone (FSH), luteinizing hormone (LH) and chorionic gonadotropin (HCG) play a critical role in human reproduction. Despite the common evolutionary ancestry and functional relatedness of the gonadotropin hormone beta (GtHB) genes, the single-copy FSHB (at 11p13) and the multi-copy LHB/CGB genes (at 19q13.32) exhibit locus-specific differences regarding their genomic context, evolution, genetic variation and expressional profile. FSHB represents a conservative vertebrate gene with a unique function and it is located in a structurally stable gene-poor region. In contrast, the primate-specific LHB/CGB gene cluster is located in a gene-rich genomic context and demonstrates an example of evolutionary young and unstable genomic region. The gene cluster is shaped by a constant balance between selection that acts on specific functions of the loci and frequent gene conversion events among duplicons. As the transcription of the GtHB genes is rate-limiting in the assembly of respective hormones, the genomic and genetic context of the FSHB and the LHB/CGB genes largely affects the profile of the hormone production.
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Affiliation(s)
- Liina Nagirnaja
- Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
| | - Kristiina Rull
- Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
- Department of Obstetrics and Gynecology, University of Tartu, Puusepa 8 G2, 51014 Tartu, Estonia
- Estonian Biocentre, Riia St. 23b, 51010 Tartu, Estonia
| | - Liis Uusküla
- Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
| | - Pille Hallast
- Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
| | - Marina Grigorova
- Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
- Estonian Biocentre, Riia St. 23b, 51010 Tartu, Estonia
| | - Maris Laan
- Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
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13
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Expression of type II chorionic gonadotropin genes supports a role in the male reproductive system. Mol Cell Biol 2010; 31:287-99. [PMID: 21078876 DOI: 10.1128/mcb.00603-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human chorionic gonadotropin (hCG) is a glycoprotein hormone essential to pregnancy. hCG is heterodimeric and functionally defined by its β subunit. hCGβ evolved from the β subunit of luteinizing hormone in two phases. In the first phase, type I genes (hCGβ3, -5, -7, and -8) acquired changes affecting gene expression and extending the proteins' C terminus. In the second phase, type II genes (hCGβ1 and -2) were formed by the insertion of a DNA element into the type I 5' end. The insertion includes the small noncoding RNA gene snaR-G and has been predicted to drastically change the protein products encoded. We trace the insertion to the common ancestor of the African great apes and show that it contains transcription signals, including snaR-G. Type II transcripts are predominantly expressed in testis. Contrary to predictions, the product of the major mRNA splice form is hCGβ. A novel peptide is encoded by alternatively spliced transcripts. These findings support the view that type II genes evolved in African great apes to function in the male reproductive system.
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Parrott AM, Tsai M, Batchu P, Ryan K, Ozer HL, Tian B, Mathews MB. The evolution and expression of the snaR family of small non-coding RNAs. Nucleic Acids Res 2010; 39:1485-500. [PMID: 20935053 PMCID: PMC3045588 DOI: 10.1093/nar/gkq856] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We recently identified the snaR family of small non-coding RNAs that associate in vivo with the nuclear factor 90 (NF90/ILF3) protein. The major human species, snaR-A, is an RNA polymerase III transcript with restricted tissue distribution and orthologs in chimpanzee but not rhesus macaque or mouse. We report their expression in human tissues and their evolution in primates. snaR genes are exclusively in African Great Apes and some are unique to humans. Two novel families of snaR-related genetic elements were found in primates: CAS (catarrhine ancestor of snaR), limited to Old World Monkeys and apes; and ASR (Alu/snaR-related), present in all monkeys and apes. ASR and CAS appear to have spread by retrotransposition, whereas most snaR genes have spread by segmental duplication. snaR-A and snaR-G2 are differentially expressed in discrete regions of the human brain and other tissues, notably including testis. snaR-A is up-regulated in transformed and immortalized human cells, and is stably bound to ribosomes in HeLa cells. We infer that snaR evolved from the left monomer of the primate-specific Alu SINE family via ASR and CAS in conjunction with major primate speciation events, and suggest that snaRs participate in tissue- and species-specific regulation of cell growth and translation.
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Affiliation(s)
- Andrew M Parrott
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, UMDNJ, Newark, New Jersey, USA
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