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Liu TT, Arango-Argoty G, Li Z, Lin Y, Kim SW, Dueck A, Ozsolak F, Monaghan AP, Meister G, DeFranco DB, John B. Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells. RNA (NEW YORK, N.Y.) 2015; 21:1159-72. [PMID: 25904138 PMCID: PMC4436668 DOI: 10.1261/rna.045559.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
The highly conserved, multifunctional YB-1 is a powerful breast cancer prognostic indicator. We report on a pervasive role for YB-1 in which it associates with thousands of nonpolyadenylated short RNAs (shyRNAs) that are further processed into small RNAs (smyRNAs). Many of these RNAs have previously been identified as functional noncoding RNAs (http://www.johnlab.org/YB1). We identified a novel, abundant, 3'-modified short RNA antisense to Dicer1 (Shad1) that colocalizes with YB-1 to P-bodies and stress granules. The expression of Shad1 was shown to correlate with that of YB-1 and whose inhibition leads to an increase in cell proliferation. Additionally, Shad1 influences the expression of additional prognostic markers of cancer progression such as DLX2 and IGFBP2. We propose that the examination of these noncoding RNAs could lead to better understanding of prostate cancer progression.
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Affiliation(s)
- Teresa T Liu
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Gustavo Arango-Argoty
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Zhihua Li
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Yuefeng Lin
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Sang Woo Kim
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Anne Dueck
- University of Regensburg, Biochemistry I, 93053 Regensburg, Bavaria, Germany
| | - Fatih Ozsolak
- Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA
| | - A Paula Monaghan
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Gunter Meister
- University of Regensburg, Biochemistry I, 93053 Regensburg, Bavaria, Germany
| | - Donald B DeFranco
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
| | - Bino John
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
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52
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Asikainen S, Heikkinen L, Juhila J, Holm F, Weltner J, Trokovic R, Mikkola M, Toivonen S, Balboa D, Lampela R, Icay K, Tuuri T, Otonkoski T, Wong G, Hovatta O. Selective microRNA-Offset RNA expression in human embryonic stem cells. PLoS One 2015; 10:e0116668. [PMID: 25822230 PMCID: PMC4378994 DOI: 10.1371/journal.pone.0116668] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/11/2014] [Indexed: 12/26/2022] Open
Abstract
Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cells (hESCs) and fibroblasts. We found that certain moRNA isoforms are notably expressed in hESCs from loci coding for stem cell-selective or cancer-related miRNA clusters. In contrast, we observed only sparse moRNAs in fibroblasts. Consistent with earlier findings, most of the observed moRNAs derived from conserved loci and their expression did not appear to correlate with the expression of the adjacent miRNAs. We provide here the first report of moRNAs in hESCs, and their expression profile in comparison to fibroblasts. Moreover, we expand the repertoire of hESC miRNAs. These findings provide an expansion on the known repertoire of small non-coding RNA contents in hESCs.
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Affiliation(s)
- Suvi Asikainen
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
- * E-mail:
| | - Liisa Heikkinen
- A.I. Virtanen Institute, University of Eastern Finland, 70211, Kuopio, Finland
- Department of Biological and Environmental Science, University of Jyvaskyla, 40014, Jyvaskyla, Finland
| | - Juuso Juhila
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Frida Holm
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Jere Weltner
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Ras Trokovic
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Milla Mikkola
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Sanna Toivonen
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Diego Balboa
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Riina Lampela
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Katherine Icay
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Timo Tuuri
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Timo Otonkoski
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland
- Children’s Hospital, Helsinki University Central Hospital, 00029, Helsinki, Finland
| | - Garry Wong
- A.I. Virtanen Institute, University of Eastern Finland, 70211, Kuopio, Finland
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., China
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden
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53
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Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc Natl Acad Sci U S A 2015; 112:E1106-15. [PMID: 25713380 DOI: 10.1073/pnas.1420955112] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two decades after the discovery of the first animal microRNA (miRNA), the number of miRNAs in animal genomes remains a vexing question. Here, we report findings from analyzing 1,323 short RNA sequencing samples (RNA-seq) from 13 different human tissue types. Using stringent thresholding criteria, we identified 3,707 statistically significant novel mature miRNAs at a false discovery rate of ≤ 0.05 arising from 3,494 novel precursors; 91.5% of these novel miRNAs were identified independently in 10 or more of the processed samples. Analysis of these novel miRNAs revealed tissue-specific dependencies and a commensurate low Jaccard similarity index in intertissue comparisons. Of these novel miRNAs, 1,657 (45%) were identified in 43 datasets that were generated by cross-linking followed by Argonaute immunoprecipitation and sequencing (Ago CLIP-seq) and represented 3 of the 13 tissues, indicating that these miRNAs are active in the RNA interference pathway. Moreover, experimental investigation through stem-loop PCR of a random collection of newly discovered miRNAs in 12 cell lines representing 5 tissues confirmed their presence and tissue dependence. Among the newly identified miRNAs are many novel miRNA clusters, new members of known miRNA clusters, previously unreported products from uncharacterized arms of miRNA precursors, and previously unrecognized paralogues of functionally important miRNA families (e.g., miR-15/107). Examination of the sequence conservation across vertebrate and invertebrate organisms showed 56.7% of the newly discovered miRNAs to be human-specific whereas the majority (94.4%) are primate lineage-specific. Our findings suggest that the repertoire of human miRNAs is far more extensive than currently represented by public repositories and that there is a significant number of lineage- and/or tissue-specific miRNAs that are uncharacterized.
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54
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Dhahbi JM. 5' tRNA Halves: The Next Generation of Immune Signaling Molecules. Front Immunol 2015; 6:74. [PMID: 25745425 PMCID: PMC4333838 DOI: 10.3389/fimmu.2015.00074] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/05/2015] [Indexed: 01/01/2023] Open
Affiliation(s)
- Joseph Mohsen Dhahbi
- Biochemistry Department, University of California Riverside , Riverside, CA , USA ; Center for Genetics, Children's Hospital Oakland Research Institute , Oakland, CA , USA
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55
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Thomson DW, Pillman KA, Anderson ML, Lawrence DM, Toubia J, Goodall GJ, Bracken CP. Assessing the gene regulatory properties of Argonaute-bound small RNAs of diverse genomic origin. Nucleic Acids Res 2015; 43:470-81. [PMID: 25452337 PMCID: PMC4288155 DOI: 10.1093/nar/gku1242] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/23/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022] Open
Abstract
High-throughput sequencing reveals an abundance of microRNA-sized fragments derived from larger non-coding RNAs. Roles for these small RNAs in gene silencing are suggested by their co-precipitation with Argonaute, the microRNA effector protein, though the extent to which they suppress gene expression endogenously remains unclear. To address this, we used luciferase reporters to determine the endogenous functionality of small RNAs from a diverse range of sources. We demonstrate small RNAs derived from snoRNAs have the capacity to act in a microRNA-like manner, though we note the vast majority of these are bound to Argonaute at levels below that required for detectable silencing activity. We show Argonaute exhibits a high degree of selectivity for the small RNAs with which it interacts and note that measuring Argonaute-associated levels is a better indicator of function than measuring total expression. Although binding to Argonaute at sufficient levels is necessary for demonstrating microRNA functionality in our reporter assay, this alone is not enough as some small RNAs derived from other non-coding RNAs (tRNAs, rRNAs, Y-RNAs) are associated with Argonaute at very high levels yet do not serve microRNA-like roles.
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Affiliation(s)
- Daniel W Thomson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Matthew L Anderson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - David M Lawrence
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Adelaide, SA 5005, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA 5005, Australia School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA 5005, Australia School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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56
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Fonseca I, Bell A, Wani K, Bell D. Global transcriptome and sequenome analysis of formalin-fixed salivary epithelial-myoepithelial carcinoma specimens. Genes Chromosomes Cancer 2014; 54:249-59. [PMID: 25546727 DOI: 10.1002/gcc.22238] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/10/2014] [Indexed: 01/09/2023] Open
Abstract
Diverse microarray and sequencing technologies have been widely used to characterize molecular changes in malignant epithelial cells in salivary neoplasms. Such gene expression studies to identify markers and targets in tumor cells are, however, compromised by the cellular heterogeneity of these tumors and by the difficulties to accrue matching controls representing normal salivary glands. Seventeen samples of primary salivary epithelial-myoepithelial carcinoma along with tissue from six normal major salivary glands were microdissected from paraffin-embedded tissue. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using a whole-transcriptome shotgun sequencing experiment. In parallel, extracted genomic DNA was used for the 50 gene hotspot panel sequenome. KRAS mutations in three patients (18%), NRAS mutations in one patient (6%), but no HRAS, MET, PIK3CA, or BRAF mutations. Using strict and conservative criteria, 220 differentially expressed transcripts were found, with 36% up- and 64% downregulated. The transcripts were annotated using NCBI Entrez Gene, and computationally analyzed with the Ingenuity Pathway Analysis program. From these significantly changed expressions, the analysis identified 26 cancer-related transcripts and 16 transcripts related to mitochondrial dysfunction overlapping with three cancer-related genes. These 220 differentially expressed genes including microRNAs provide here a sufficiently large set to specifically define epithelial-myoepithelial carcinoma and to identify novel and potentially important targets for diagnosis, prognosis, and therapy of this cancer.
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Affiliation(s)
- Isabel Fonseca
- Serviço de Anatomia Patológica, Instituto Português de Oncologia Francisco Gentil, Lisboa, Portugal & Instituto de Anatomia Patológica, Faculdade de Medicina de Lisboa, Portugal
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57
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Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Martin DI. Deep Sequencing of Serum Small RNAs Identifies Patterns of 5' tRNA Half and YRNA Fragment Expression Associated with Breast Cancer. BIOMARKERS IN CANCER 2014; 6:37-47. [PMID: 25520563 PMCID: PMC4260766 DOI: 10.4137/bic.s20764] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/14/2014] [Accepted: 11/17/2014] [Indexed: 12/18/2022]
Abstract
Small noncoding RNAs circulating in the blood may serve as signaling molecules because of their ability to carry out a variety of cellular functions. We have previously described tRNA- and YRNA-derived small RNAs circulating as components of larger complexes in the blood of humans and mice; the characteristics of these small RNAs imply specific processing, secretion, and physiological regulation. In this study, we have asked if changes in the serum abundance of these tRNA and YRNA fragments are associated with a diagnosis of cancer. We used deep sequencing and informatics analysis to catalog small RNAs in the sera of breast cancer cases and normal controls. 5′ tRNA halves and YRNA fragments are abundant in both groups, but we found that a breast cancer diagnosis is associated with changes in levels of specific subtypes. This prompted us to look at existing sequence datasets of serum small RNAs from 42 breast cancer cases, taken at the time of diagnosis. We find significant changes in the levels of specific 5′ tRNA halves and YRNA fragments associated with clinicopathologic characteristics of the cancer. Although these findings do not establish causality, they suggest that circulating 5′ tRNA halves and YRNA fragments with known cellular functions may participate in breast cancer syndromes and have potential as circulating biomarkers. Larger studies with multiple types of cancer are needed to adequately evaluate their potential use for the development of noninvasive cancer screening.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA. ; Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Stephen R Spindler
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Hani Atamna
- Department of Medical Education, California Northstate University, Elk Grove, CA, USA
| | - Dario Boffelli
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - David Ik Martin
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
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58
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Beatty M, Guduric-Fuchs J, Brown E, Bridgett S, Chakravarthy U, Hogg RE, Simpson DA. Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma. BMC Genomics 2014; 15:933. [PMID: 25344700 PMCID: PMC4230795 DOI: 10.1186/1471-2164-15-933] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 10/16/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived. RESULTS Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin. In addition, extremely abundant small RNAs derived from human Y RNAs were detected. CONCLUSIONS A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.
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Affiliation(s)
| | | | | | | | | | | | - David Arthur Simpson
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.
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59
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Avitabile C, Cimmino A, Romanelli A. Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications. J Med Chem 2014; 57:10220-40. [PMID: 25280271 DOI: 10.1021/jm5006594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
ncRNAs are emerging as key regulators of physiological and pathological processes and therefore have been identified as pharmacological targets and as markers for some diseases. Oligonucleotide analogues represent so far the most widely employed tool for the modulation of the expression of ncRNAs. In this perspective we briefly describe most of the known classes of ncRNAs and then we discuss the design and the applications of oligonucleotide analogues for their targeting. The effects of modifications of the chemical structure of the oligonucleotides on properties such as the binding affinity toward targets and off targets, and the stability to degradation and their biological effects (when known) are discussed. Examples of molecules currently used in clinical trials are also reported.
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Affiliation(s)
- Concetta Avitabile
- Università di Napoli "Federico II" , Dipartimento di Farmacia, via Mezzocannone 16, 80134 Napoli, Italy
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60
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Dhahbi JM. Circulating small noncoding RNAs as biomarkers of aging. Ageing Res Rev 2014; 17:86-98. [PMID: 24607831 DOI: 10.1016/j.arr.2014.02.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 12/31/2022]
Abstract
Small noncoding RNAs (sncRNAs) mediate a variety of cellular functions in animals and plants. Deep sequencing has made it possible to obtain highly detailed information on the types and abundance of sncRNAs in biological specimens, leading to the discovery that sncRNAs circulate in the blood of humans and mammals. The most abundant types of circulating sncRNAs are microRNAs (miRNAs), 5' transfer RNA (tRNA) halves, and YRNA fragments, with minute amounts of other types that may nevertheless be significant. Of the more abundant circulating sncRNAs only miRNAs have well described functions, but characteristics of the others suggest specific processing and secretion as complexes that protect the RNA from degradation. The properties of circulating sncRNAs are consistent with their serving as signaling molecules, and investigations of circulating miRNAs support the view that they can enter cells and regulate cellular functions. The serum levels of specific sncRNAs change markedly with age, and these changes can be mitigated by calorie restriction (CR), indicating that levels are under physiologic control. The ability of circulating sncRNAs to transmit functions between cells and to regulate a broad spectrum of cellular functions, and the changes in their levels with age, implicate them in the manifestations of aging. Our understanding of the functions of circulating sncRNA, particularly in relation to aging, is currently at a very early stage; results to date suggest that more extensive investigation will yield important insights into mechanisms of aging.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA; Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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61
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Desvignes T, Beam MJ, Batzel P, Sydes J, Postlethwait JH. Expanding the annotation of zebrafish microRNAs based on small RNA sequencing. Gene 2014; 546:386-9. [PMID: 24835514 PMCID: PMC4130647 DOI: 10.1016/j.gene.2014.05.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/29/2014] [Accepted: 05/14/2014] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. Because of their role in the regulation of gene expression, miRs are essential players in development by acting on cell fate determination and progression towards cell differentiation and are increasingly relevant to human health and disease. Although the zebrafish Danio rerio is a major model for studies of development, genetics, physiology, evolution, and human biology, the annotation of zebrafish miR-producing genes remains limited. In the present work, we report deep sequencing data of zebrafish small RNAs from brain, heart, testis, and ovary. Results provide evidence for the expression of 56 un-annotated mir genes and 248 un-annotated mature strands, increasing the number of zebrafish mir genes over those already deposited in miRBase by 16% and the number of mature sequences by 63%. We also describe the existence of three pairs of mirror-mir genes and two mirtron genes, genetic features previously undescribed in non-mammalian vertebrates. This report provides information that substantially increases our knowledge of the zebrafish miRNome and will benefit the entire miR community.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
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62
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Li E, Ji P, Ouyang N, Zhang Y, Wang XY, Rubin DC, Davidson NO, Bergamaschi R, Shroyer KR, Burke S, Zhu W, Williams JL. Differential expression of miRNAs in colon cancer between African and Caucasian Americans: implications for cancer racial health disparities. Int J Oncol 2014; 45:587-94. [PMID: 24865442 PMCID: PMC4091964 DOI: 10.3892/ijo.2014.2469] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/26/2014] [Indexed: 01/04/2023] Open
Abstract
Colorectal cancer (CRC) incidence and mortality are higher in African Americans (AAs) than in Caucasian Americans (CAs) and microRNAs (miRNAs) have been found to be dysregulated in colonic and other neoplasias. The aim of this exploratory study was to identify candidate miRNAs that could contribute to potential biological differences between AA and CA colon cancers. Total RNA was isolated from tumor and paired adjacent normal colon tissue from 30 AA and 31 CA colon cancer patients archived at Stony Brook University (SBU) and Washington University (WU)‑St. Louis Medical Center. miRNA profiles were determined by probing human genome-wide miRNA arrays with RNA isolated from each sample. Using repeated measures analysis of variance (RANOVA), miRNAs were selected that exhibited significant (p<0.05) interactions between race and tumor or significant (fold change >1.5, p<0.05) main effects of race and/or tumor. Quantitative polymerase chain reaction (q-PCR) was used to confirm miRNAs identified by microarray analysis. Candidate miRNA targets were analyzed using immunohistochemistry. RANOVA results indicated that miR-182, miR152, miR-204, miR-222 and miR-202 exhibited significant race and tumor main effects. Of these miRNAs, q-PCR analysis confirmed that miR-182 was upregulated in AA vs. CA tumors and exhibited significant race:tumor interaction. Immunohistochemical analysis revealed that the levels of FOXO1 and FOXO3A, two potential miR-182 targets, are reduced in AA tumors. miRNAs may play a role in the differences between AA and CA colon cancer. Specifically, differences in miRNA expression levels of miR-182 may contribute to decreased survival in AA colon cancer patients.
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Affiliation(s)
- Ellen Li
- Division of Gastroenterology, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Ping Ji
- Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Nengtai Ouyang
- Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Yuanhao Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Xin Yu Wang
- Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Deborah C Rubin
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas O Davidson
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Roberto Bergamaschi
- Division of Colon and Rectal Surgery, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Kenneth R Shroyer
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Stephanie Burke
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Wei Zhu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-8160, USA
| | - Jennie L Williams
- Division of Cancer Prevention, Stony Brook University, Stony Brook, NY 11794-8160, USA
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Chen D, Fu LY, Zhang Z, Li G, Zhang H, Jiang L, Harrison AP, Shanahan HP, Klukas C, Zhang HY, Ruan Y, Chen LL, Chen M. Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res 2014; 42:3028-43. [PMID: 24357409 PMCID: PMC3950692 DOI: 10.1093/nar/gkt1294] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 12/19/2022] Open
Abstract
Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs. We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II-associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA-target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR-MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.
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Affiliation(s)
- Dijun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Liang-Yu Fu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Zhao Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Guoliang Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Hang Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Li Jiang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Andrew P. Harrison
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Hugh P. Shanahan
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Christian Klukas
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Hong-Yu Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Yijun Ruan
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Ling-Ling Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
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Yamazaki F, Kim HH, Lau P, Hwang CK, Iuvone PM, Klein D, Clokie SJH. pY RNA1-s2: a highly retina-enriched small RNA that selectively binds to Matrin 3 (Matr3). PLoS One 2014; 9:e88217. [PMID: 24558381 PMCID: PMC3928194 DOI: 10.1371/journal.pone.0088217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/03/2014] [Indexed: 12/22/2022] Open
Abstract
The purpose of this study was to expand our knowledge of small RNAs, which are known to function within protein complexes to modulate the transcriptional output of the cell. Here we describe two previously unrecognized, small RNAs, termed pY RNA1-s1 and pY RNA1-s2 (processed Y RNA1-stem −1 and −2), thereby expanding the list of known small RNAs. pY RNA1-s1 and pY RNA1-s2 were discovered by RNA sequencing and found to be 20-fold more abundant in the retina than in 14 other rat tissues. Retinal expression of pY RNAs is highly conserved, including expression in the human retina, and occurs in all retinal cell layers. Mass spectrometric analysis of pY RNA1-S2 binding proteins in retina indicates that pY RNA1-s2 selectively binds the nuclear matrix protein Matrin 3 (Matr3) and to a lesser degree to hnrpul1 (heterogeneous nuclear ribonucleoprotein U-like protein). In contrast, pY RNA1-s1 does not bind these proteins. Accordingly, the molecular mechanism of action of pY RNA1-s2 is likely be through an action involving Matr3; this 95 kDa protein has two RNA recognition motifs (RRMs) and is implicated in transcription and RNA-editing. The high affinity binding of pY RNA1-s2 to Matr3 is strongly dependent on the sequence of the RNA and both RRMs of Matr3. Related studies also indicate that elements outside of the RRM region contribute to binding specificity and that phosphorylation enhances pY RNA-s2/Matr3 binding. These observations are of significance because they reveal that a previously unrecognized small RNA, pY RNA1-s2, binds selectively to Matr3. Hypothetically, pY RNA1-S2 might act to modulate cellular function through this molecular mechanism. The retinal enrichment of pY RNA1-s2 provides reason to suspect that the pY RNA1-s2/Matr3 interaction could play a role in vision.
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Affiliation(s)
- Fumiyoshi Yamazaki
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hyun Hee Kim
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Pierre Lau
- Division of intramural research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher K. Hwang
- Departments of Ophthalmology and Pharmacology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - P. Michael Iuvone
- Departments of Ophthalmology and Pharmacology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - David Klein
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Samuel J. H. Clokie
- Section on Neuroendocrinology, Program in Developmental Endocrinology and Genetics, The Eunice Shriver Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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Abstract
The different RNA populations within the cell, or the 'RNAome', form a complex and integral layer of gene regulation. In particular, small non-coding RNAs such as microRNAs have been shown to regulate as much as half of all genes expressed in mammals. The recent discovery of novel small RNAs derived from tRNAs, snoRNAs and Y RNAs, as well as the development of techniques that can reduce sequencing bias of these molecules, is slowly helping us to unveil the secrets of the genome.
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Links between the oncoprotein YB-1 and small non-coding RNAs in breast cancer. PLoS One 2013; 8:e80171. [PMID: 24260353 PMCID: PMC3832415 DOI: 10.1371/journal.pone.0080171] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/07/2013] [Indexed: 12/21/2022] Open
Abstract
Background The nucleic acid-binding protein YB-1, a member of the cold-shock domain protein family, has been implicated in the progression of breast cancer and is associated with poor patient survival. YB-1 has sequence similarity to LIN28, another cold-shock protein family member, which has a role in the regulation of small noncoding RNAs (sncRNAs) including microRNAs (miRNAs). Therefore, to investigate whether there is an association between YB-1 and sncRNAs in breast cancer, we investigated whether sncRNAs were bound by YB-1 in two breast cancer cell lines (luminal A-like and basal cell-like), and whether the abundance of sncRNAs and mRNAs changed in response to experimental reduction of YB-1 expression. Results RNA-immunoprecipitation with an anti-YB-1 antibody showed that several sncRNAs are bound by YB-1. Some of these were bound by YB-1 in both breast cancer cell lines; others were cell-line specific. The small RNAs bound by YB-1 were derived from various sncRNA families including miRNAs such as let-7 and miR-320, transfer RNAs, ribosomal RNAs and small nucleolar RNAs (snoRNA). Reducing YB-1 expression altered the abundance of a number of transcripts encoding miRNA biogenesis and processing proteins but did not alter the abundance of mature or precursor miRNAs. Conclusions YB-1 binds to specific miRNAs, snoRNAs and tRNA-derived fragments and appears to regulate the expression of miRNA biogenesis and processing machinery. We propose that some of the oncogenic effects of YB-1 in breast cancer may be mediated through its interactions with sncRNAs.
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Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Mote P, Martin DIK. 5′-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. Physiol Genomics 2013; 45:990-8. [DOI: 10.1152/physiolgenomics.00129.2013] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small noncoding RNAs carry out a variety of functions in eukaryotic cells, and in multiple species they can travel between cells, thus serving as signaling molecules. In mammals multiple small RNAs have been found to circulate in the blood, although in most cases the targets of these RNAs, and even their functions, are not well understood. YRNAs are small (84–112 nt) RNAs with poorly characterized functions, best known because they make up part of the Ro ribonucleoprotein autoantigens in connective tissue diseases. In surveying small RNAs present in the serum of healthy adult humans, we have found YRNA fragments of lengths 27 nt and 30–33 nt, derived from the 5′-ends of specific YRNAs and generated by cleavage within a predicted internal loop. Many of the YRNAs from which these fragments are derived were previously annotated only as pseudogenes, or predicted informatically. These 5′-YRNA fragments make up a large proportion of all small RNAs (including miRNAs) present in human serum. They are also present in plasma, are not present in exosomes or microvesicles, and circulate as part of a complex with a mass between 100 and 300 kDa. Mouse serum contains far fewer 5′-YRNA fragments, possibly reflecting the much greater copy number of YRNA genes and pseudogenes in humans. The function of the 5′-YRNA fragments is at present unknown, but the processing and secretion of specific YRNAs to produce 5′-end fragments that circulate in stable complexes are consistent with a signaling function.
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Affiliation(s)
- Joseph M. Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - Stephen R. Spindler
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - Hani Atamna
- Department of Basic Sciences, Neuroscience, The Commonwealth Medical College, Scranton, Pennsylvania
| | - Dario Boffelli
- Center for Genetics, Childrens Hospital Oakland Research Institute, Oakland, California
| | - Patricia Mote
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - David I. K. Martin
- Center for Genetics, Childrens Hospital Oakland Research Institute, Oakland, California
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68
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Chen CJ, Heard E. Small RNAs derived from structural non-coding RNAs. Methods 2013; 63:76-84. [DOI: 10.1016/j.ymeth.2013.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 04/12/2013] [Accepted: 05/06/2013] [Indexed: 12/25/2022] Open
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Perez P, Jang SI, Alevizos I. Emerging landscape of non-coding RNAs in oral health and disease. Oral Dis 2013; 20:226-35. [PMID: 23781896 DOI: 10.1111/odi.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022]
Abstract
The world of non-coding RNAs has only recently started being discovered. For the past 40 years, coding genes, mRNA, and proteins have been the center of cellular and molecular biology, and pathologic alterations were attributed to either the aberration of gene sequence or altered promoter activity. It was only after the completion of the human genome sequence that the scientific community started seriously wondering why only a very small portion of the genome corresponded to protein-coding genes. New technologies such as the whole-genome and whole-transcriptome sequencing demonstrated that at least 90% of the genome is actively transcribed. The identification and cataloguing of multiple kinds of non-coding RNA (ncRNA) have exponentially increased, and it is now widely accepted that ncRNAs play major biological roles in cellular physiology, development, metabolism, and are also implicated in a variety of diseases. The aim of this review is to describe the two major classes (long and short forms) of non-coding RNAs and describe their subclasses in terms of function and their relevance and potential in oral diseases.
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Affiliation(s)
- P Perez
- Sjögren's Clinic, Molecular Physiology & Therapeutics, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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Mor E, Kano SI, Colantuoni C, Sawa A, Navon R, Shomron N. MicroRNA-382 expression is elevated in the olfactory neuroepithelium of schizophrenia patients. Neurobiol Dis 2013; 55:1-10. [PMID: 23542694 DOI: 10.1016/j.nbd.2013.03.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/17/2013] [Accepted: 03/20/2013] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia is a common neuropsychiatric disorder that has a strong genetic component. MicroRNAs (miRNAs) have been implicated in neurodevelopmental and psychiatric disorders including schizophrenia, as indicated by their dysregulation in post-mortem brain tissues and in peripheral blood of schizophrenia patients. The olfactory epithelium (OE) is one of the few accessible neural tissues that contain neurons and their stem cells. Previous studies showed that OE-derived tissues and cells can be safely and easily collected from live human subjects and may provide a "window" into neuronal processes involved in disorders such as schizophrenia, while avoiding the limitations of using postmortem brain samples or non-neuronal tissues. In this study, we found that the brain-enriched miR-382 (miR-382-5p) expression was elevated in in vitro cultured olfactory cells, in a cohort of seven schizophrenia patients compared with seven non-schizophrenic controls. MiR-382 elevation was further confirmed in laser-capture microdissected OE neuronal tissue (LCM-OE), enriched for mature olfactory neurons, in a cohort of 18 schizophrenia patients and 18 non-schizophrenic controls. In sharp contrast, miR-382 expression could not be detected in lymphoblastoid cell lines generated from schizophrenic or non-schizophrenic individuals. We further found that miR-382 directly regulates the expression of two genes, FGFR1 and SPRY4, which are downregulated in both the cultured olfactory cells and LCM-OE derived from schizophrenia patients. These genes are involved in the fibroblast growth factor (FGF) signaling pathway, while impairment of this pathway may underlie abnormal brain development and function associated with schizophrenia. Our data suggest that miR-382 elevation detected in patients' OE-derived samples might serve to strengthen current biomarker studies in schizophrenia. This study also illustrates the potential utility of OE-derived tissues and cells as surrogate samples for the brain.
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Affiliation(s)
- Eyal Mor
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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71
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Leptidis S, el Azzouzi H, Lok SI, de Weger R, Olieslagers S, Kisters N, Silva GJ, Heymans S, Cuppen E, Berezikov E, De Windt LJ, da Costa Martins P. A deep sequencing approach to uncover the miRNOME in the human heart. PLoS One 2013; 8:e57800. [PMID: 23460909 PMCID: PMC3583901 DOI: 10.1371/journal.pone.0057800] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 01/29/2013] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs of ∼22 nucleotides in length, and constitute a novel class of gene regulators by imperfect base-pairing to the 3′UTR of protein encoding messenger RNAs. Growing evidence indicates that miRNAs are implicated in several pathological processes in myocardial disease. The past years, we have witnessed several profiling attempts using high-density oligonucleotide array-based approaches to identify the complete miRNA content (miRNOME) in the healthy and diseased mammalian heart. These efforts have demonstrated that the failing heart displays differential expression of several dozens of miRNAs. While the total number of experimentally validated human miRNAs is roughly two thousand, the number of expressed miRNAs in the human myocardium remains elusive. Our objective was to perform an unbiased assay to identify the miRNOME of the human heart, both under physiological and pathophysiological conditions. We used deep sequencing and bioinformatics to annotate and quantify microRNA expression in healthy and diseased human heart (heart failure secondary to hypertrophic or dilated cardiomyopathy). Our results indicate that the human heart expresses >800 miRNAs, the majority of which not being annotated nor described so far and some of which being unique to primate species. Furthermore, >250 miRNAs show differential and etiology-dependent expression in human dilated cardiomyopathy (DCM) or hypertrophic cardiomyopathy (HCM). The human cardiac miRNOME still possesses a large number of miRNAs that remain virtually unexplored. The current study provides a starting point for a more comprehensive understanding of the role of miRNAs in regulating human heart disease.
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Affiliation(s)
- Stefanos Leptidis
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Hamid el Azzouzi
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Sjoukje I. Lok
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel de Weger
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Serv Olieslagers
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Natasja Kisters
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Gustavo J. Silva
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Stephane Heymans
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Royal Netherlands Academy of Sciences, Utrecht, The Netherlands
| | - Eugene Berezikov
- Hubrecht Institute, Royal Netherlands Academy of Sciences, Utrecht, The Netherlands
| | - Leon J. De Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Paula da Costa Martins
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- * E-mail:
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Munch EM, Harris RA, Mohammad M, Benham AL, Pejerrey SM, Showalter L, Hu M, Shope CD, Maningat PD, Gunaratne PH, Haymond M, Aagaard K. Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk. PLoS One 2013; 8:e50564. [PMID: 23418415 PMCID: PMC3572105 DOI: 10.1371/journal.pone.0050564] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/22/2012] [Indexed: 01/06/2023] Open
Abstract
While breast milk has unique health advantages for infants, the mechanisms by which it regulates the physiology of newborns are incompletely understood. miRNAs have been described as functioning transcellularly, and have been previously isolated in cell-free and exosomal form from bodily liquids (serum, saliva, urine) and tissues, including mammary tissue. We hypothesized that breast milk in general, and milk fat globules in particular, contain significant numbers of known and limited novel miRNA species detectable with massively parallel sequencing. Extracted RNA from lactating mothers before and following short-term treatment with recombinant human growth hormone (rhGH) was smRNA-enriched. smRNA-Seq was performed to generate 124,110,646 36-nt reads. Of these, 31,102,927 (25%) exactly matched known human miRNAs; with relaxing of stringency, 74,716,151 (60%) matched known miRNAs including 308 of the 1018 (29%) mature miRNAs (miRBase 16.0). These miRNAs are predicted to target 9074 genes; the 10 most abundant of these predicted to target 2691 genes with enrichment for transcriptional regulation of metabolic and immune responses. We identified 21 putative novel miRNAs, of which 12 were confirmed in a large validation set that included cohorts of lactating women consuming enriched diets. Of particular interest, we observed that expression of several novel miRNAs were altered by the perturbed maternal diet, notably following a high-fat intake (p<0.05). Our findings suggest that known and novel miRNAs are enriched in breast milk fat globules, and expression of several novel miRNA species is regulated by maternal diet. Based on robust pathway mapping, our data supports the notion that these maternally secreted miRNAs (stable in the milk fat globules) play a regulatory role in the infant and account in part for the health benefits of breast milk. We further speculate that regulation of these miRNA by a high fat maternal diet enables modulation of fetal metabolism to accommodate significant dietary challenges.
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Affiliation(s)
- Erika M. Munch
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mahmoud Mohammad
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Baylor College of Medicine, Texas Children’s Hospital, The Children’s Nutrition Research Center, US Department of Agriculture, Agricultural Research Service, Houston, Texas, United States of America
| | - Ashley L. Benham
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Sasha M. Pejerrey
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lori Showalter
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Min Hu
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Cynthia D. Shope
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Patricia D. Maningat
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Baylor College of Medicine, Texas Children’s Hospital, The Children’s Nutrition Research Center, US Department of Agriculture, Agricultural Research Service, Houston, Texas, United States of America
| | - Preethi H. Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Morey Haymond
- Department of Pediatrics, Division of Pediatric Endocrinology and Metabolism, Baylor College of Medicine, Texas Children’s Hospital, The Children’s Nutrition Research Center, US Department of Agriculture, Agricultural Research Service, Houston, Texas, United States of America
| | - Kjersti Aagaard
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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73
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Köhn M, Pazaitis N, Hüttelmaier S. Why YRNAs? About Versatile RNAs and Their Functions. Biomolecules 2013; 3:143-56. [PMID: 24970161 PMCID: PMC4030889 DOI: 10.3390/biom3010143] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 01/27/2013] [Accepted: 01/31/2013] [Indexed: 11/20/2022] Open
Abstract
Y RNAs constitute a family of highly conserved small noncoding RNAs (in humans: 83-112 nt; Y1, Y3, Y4 and Y5). They are transcribed from individual genes by RNA-polymerase III and fold into conserved stem-loop-structures. Although discovered 30 years ago, insights into the cellular and physiological role of Y RNAs remains incomplete. In this review, we will discuss knowledge on the structural properties, associated proteins and discuss proposed functions of Y RNAs. We suggest Y RNAs to be an integral part of ribonucleoprotein networks within cells and could therefore have substantial influence on many different cellular processes. Putative functions of Y RNAs include small RNA quality control, DNA replication, regulation of the cellular stress response and proliferation. This suggests Y RNAs as essential regulators of cell fate and indicates future avenues of research, which will provide novel insights into the role of small noncoding RNAs in gene expression.
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Affiliation(s)
- Marcel Köhn
- Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, Section Molecular Cell Biology, ZAMED, Heinrich-Damerow-Str.1, D-6120 Halle, Germany.
| | - Nikolaos Pazaitis
- Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, Section Molecular Cell Biology, ZAMED, Heinrich-Damerow-Str.1, D-6120 Halle, Germany.
| | - Stefan Hüttelmaier
- Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, Section Molecular Cell Biology, ZAMED, Heinrich-Damerow-Str.1, D-6120 Halle, Germany.
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74
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Sato Y, Toriyabe Y, Nishizawa S, Teramae N. 2,4-Diamino-6,7-dimethylpteridine as a fluorescent ligand for binding and sensing an orphan cytosine in RNA duplexes. Chem Commun (Camb) 2013; 49:9983-5. [DOI: 10.1039/c3cc46085a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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75
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Jorge NAN, Ferreira CG, Passetti F. Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges. Front Genet 2012; 3:287. [PMID: 23251139 PMCID: PMC3523245 DOI: 10.3389/fgene.2012.00287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/22/2012] [Indexed: 12/24/2022] Open
Abstract
The numerous genome sequencing projects produced unprecedented amount of data providing significant information to the discovery of novel non-coding RNA (ncRNA). Several ncRNAs have been described to control gene expression and display important role during cell differentiation and homeostasis. In the last decade, high throughput methods in conjunction with approaches in bioinformatics have been used to identify, classify, and evaluate the expression of hundreds of ncRNA in normal and pathological states, such as cancer. Patient outcomes have been already associated with differential expression of ncRNAs in normal and tumoral tissues, providing new insights in the development of innovative therapeutic strategies in oncology. In this review, we present and discuss bioinformatics advances in the development of computational approaches to analyze and discover ncRNA data in oncology using high throughput sequencing technologies.
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76
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Langenberger D, Çakir MV, Hoffmann S, Stadler PF. Dicer-processed small RNAs: rules and exceptions. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 320:35-46. [PMID: 23165937 DOI: 10.1002/jez.b.22481] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/15/2012] [Accepted: 09/13/2012] [Indexed: 01/08/2023]
Abstract
Canonical microRNAs are excised from their hairpin-shaped precursors by Dicer. In order to find possible exceptions to this rule and to identify additional substrates for Dicer processing we re-evaluate the small RNA sequencing data of the Dicer knockdown experiment in MCF-7 cells orignally published by Friedländer et al. [Friedländer et al., 2012, Nucleic Acids Res 40:37-52]. While the well-known non-Dicer mir-451 is not sufficiently expressed in these experiments, there are several additional Dicer-independent microRNAs, among them the important tumor supressor mir-663a. We recover previously described examples of non-miRNA Dicer substrates such as tRNA-Gln and several snoRNAs. Interestingly, sdRNAs derived from box C/D snoRNAs are Dicer-independent, while those derived from box H/ACA snoRNAs are often Dicer dependent. Several pol-III transcripts, in particular the vault RNAs and the great ape specific snaRs are processed by Dicer, while the small RNAs originating from Y RNAs seem to be Dicer independent.
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Affiliation(s)
- David Langenberger
- LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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77
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Yun SJ, Jeong P, Kim WT, Kim TH, Lee YS, Song PH, Choi YH, Kim IY, Moon SK, Kim WJ. Cell-free microRNAs in urine as diagnostic and prognostic biomarkers of bladder cancer. Int J Oncol 2012; 41:1871-8. [PMID: 22961325 DOI: 10.3892/ijo.2012.1622] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 08/20/2012] [Indexed: 11/05/2022] Open
Abstract
miRNAs are small, non-coding RNAs that play important roles in various biological processes. The aims of our study were to investigate whether cell-free miRNAs can be measured in urine samples and might be an accurate biomarker of bladder cancer. Datasets of GSE20418 and GSE19717 were used for analysis, and two miRNAs, miR-145 and miR-200a, were selected for study. A total of 207 patients with primary transitional cell carcinoma of the urinary bladder and 144 healthy normal controls were enrolled. Using quantitative PCR, the levels of miR-145 and miR-200a in urine were measured and compared with the clinicopathological features of bladder cancer. According to our experiments, cell-free miRNAs were present in urine and were stable. Assessment of miR-145 levels was able to distinguish bladder cancer patients from non-cancer controls (77.8% sensitivity and 61.1% specificity for NMIBC, AUC 0.729; 84.1 and 61.1% for MIBC, respectively, AUC 0.790) and showed good correlation with grade (p=0.048). In addition, miR-200a was shown to be an independent predictor of NMIBC recurrence by multivariate analysis (OR 0.449, 95% CI 0.239‑0.842, p=0.013). A higher risk of recurrence was observed among patients with a lower miR-200a level compared to patients with higher miR-200a levels (log-rank test, p=0.040). Urinary cell-free miRNAs show promise as noninvasive biomarkers for diagnosis and recurrence of bladder cancer.
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Affiliation(s)
- Seok Joong Yun
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
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Lin Y, Li Z, Ozsolak F, Kim SW, Arango-Argoty G, Liu TT, Tenenbaum SA, Bailey T, Monaghan AP, Milos PM, John B. An in-depth map of polyadenylation sites in cancer. Nucleic Acids Res 2012; 40:8460-71. [PMID: 22753024 PMCID: PMC3458571 DOI: 10.1093/nar/gks637] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 05/16/2012] [Accepted: 06/06/2012] [Indexed: 12/22/2022] Open
Abstract
We present a comprehensive map of over 1 million polyadenylation sites and quantify their usage in major cancers and tumor cell lines using direct RNA sequencing. We built the Expression and Polyadenylation Database to enable the visualization of the polyadenylation maps in various cancers and to facilitate the discovery of novel genes and gene isoforms that are potentially important to tumorigenesis. Analyses of polyadenylation sites indicate that a large fraction (∼30%) of mRNAs contain alternative polyadenylation sites in their 3' untranslated regions, independent of the cell type. The shortest 3' untranslated region isoforms are preferentially upregulated in cancer tissues, genome-wide. Candidate targets of alternative polyadenylation-mediated upregulation of short isoforms include POLR2K, and signaling cascades of cell-cell and cell-extracellular matrix contact, particularly involving regulators of Rho GTPases. Polyadenylation maps also helped to improve 3' untranslated region annotations and identify candidate regulatory marks such as sequence motifs, H3K36Me3 and Pabpc1 that are isoform dependent and occur in a position-specific manner. In summary, these results highlight the need to go beyond monitoring only the cumulative transcript levels for a gene, to separately analysing the expression of its RNA isoforms.
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Affiliation(s)
- Yuefeng Lin
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Zhihua Li
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Fatih Ozsolak
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Sang Woo Kim
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Gustavo Arango-Argoty
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Teresa T. Liu
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Scott A. Tenenbaum
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Timothy Bailey
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - A. Paula Monaghan
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Patrice M. Milos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Bino John
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
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79
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Zaravinos A, Radojicic J, Lambrou GI, Volanis D, Delakas D, Stathopoulos EN, Spandidos DA. Expression of miRNAs Involved in Angiogenesis, Tumor Cell Proliferation, Tumor Suppressor Inhibition, Epithelial-Mesenchymal Transition and Activation of Metastasis in Bladder Cancer. J Urol 2012; 188:615-23. [DOI: 10.1016/j.juro.2012.03.122] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Indexed: 11/27/2022]
Affiliation(s)
- Apostolos Zaravinos
- Laboratory of Virology, Medical School, University of Crete, Heraklion, Greece
| | - Jelena Radojicic
- Department of Surgical Pathology, Medical Faculty, University of Crete, Heraklion, Greece
| | - George I. Lambrou
- First Department of Pediatrics, Choremeio Research Laboratory, University of Athens, Greece
| | - Dimitrios Volanis
- Laboratory of Virology, Medical School, University of Crete, Heraklion, Greece
- Department of Urology, Asklipieio General Hospital, Athens, Greece
| | - Dimitris Delakas
- Department of Urology, Asklipieio General Hospital, Athens, Greece
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80
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Enfield KSS, Pikor LA, Martinez VD, Lam WL. Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications. GENETICS RESEARCH INTERNATIONAL 2012; 2012:737416. [PMID: 22852089 PMCID: PMC3407615 DOI: 10.1155/2012/737416] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 03/08/2012] [Indexed: 01/07/2023]
Abstract
Lung cancer biology has traditionally focused on genomic and epigenomic deregulation of protein-coding genes to identify oncogenes and tumor suppressors diagnostic and therapeutic targets. Another important layer of cancer biology has emerged in the form of noncoding RNAs (ncRNAs), which are major regulators of key cellular processes such as proliferation, RNA splicing, gene regulation, and apoptosis. In the past decade, microRNAs (miRNAs) have moved to the forefront of ncRNA cancer research, while the role of long noncoding RNAs (lncRNAs) is emerging. Here we review the mechanisms by which miRNAs and lncRNAs are deregulated in lung cancer, the technologies that can be applied to detect such alterations, and the clinical potential of these RNA species. An improved comprehension of lung cancer biology will come through the understanding of the interplay between deregulation of non-coding RNAs, the protein-coding genes they regulate, and how these interactions influence cellular networks and signalling pathways.
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Affiliation(s)
- Katey S. S. Enfield
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada V5Z1L3
| | - Larissa A. Pikor
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada V5Z1L3
| | - Victor D. Martinez
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V6T2B5
| | - Wan L. Lam
- British Columbia Cancer Research Center, Vancouver, BC, Canada V5Z 1L3
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada V5Z1L3
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V6T2B5
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81
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Characterization and discovery of novel miRNAs and moRNAs in JAK2V617F-mutated SET2 cells. Blood 2012; 119:e120-30. [DOI: 10.1182/blood-2011-07-368001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
To gain insights into a possible role of microRNAs in myeloproliferative neoplasms, we performed short RNA massive sequencing and extensive bioinformatic analysis in the JAK2V617F-mutated SET2 cell line. Overall, 652 known mature miRNAs were detected, of which 21 were highly expressed, thus being responsible of most of miRNA-mediated gene repression. microRNA putative targets were enriched in specific signaling pathways, providing information about cell activities under massive posttranscriptional regulation. The majority of miRNAs were mixtures of sequence variants, called isomiRs, mainly because of alternative, noncanonical processing of hairpin precursors. We also identified 78 novel miRNAs (miRNA*) derived from known hairpin precursors. Both major and minor (*) forms of miRNAs were expressed concurrently from half of expressed hairpins, highlighting the relevance of miRNA* and the complexity of strand selection bias regulation. Finally, we discovered that SET2 cells express a number of miRNA-offset RNAs (moRNAs), short RNAs derived from genomic regions flanking mature miRNAs. We provide novel data about the possible origin of moRNAs, although their functional role remains to be elucidated. Overall, this study shed light on the complexity of microRNA-mediated gene regulation in SET2 cells and represents the basis for future studies in JAK2V617F-mutated cellular models.
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82
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Nicolas FE, Hall AE, Csorba T, Turnbull C, Dalmay T. Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway. FEBS Lett 2012; 586:1226-30. [PMID: 22575660 DOI: 10.1016/j.febslet.2012.03.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 12/30/2022]
Abstract
Y RNAs are approximately 100 nucleotide long conserved cytoplasmic non-coding RNAs, which produce smaller RNA fragments during apoptosis. Here we show that these smaller RNA molecules are also produced in non-stressed cells and in a range of human cancerous and non-cancerous cell types. Recent reports have speculated that the cleavage products of Y RNAs enter the microRNA pathway. We tested this hypothesis and found that Y5 and Y3 RNA fragments are Dicer independent, they are in different complexes than microRNAs and that they are not co-immunoprecipitated with Ago2. Therefore we conclude that Y RNA fragments do not enter the microRNA pathway.
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83
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Zhang X, Wang H, Zhang S, Song J, Zhang Y, Wei X, Feng Z. MiR-134 functions as a regulator of cell proliferation, apoptosis, and migration involving lung septation. In Vitro Cell Dev Biol Anim 2012; 48:131-6. [PMID: 22259016 DOI: 10.1007/s11626-012-9482-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/02/2012] [Indexed: 12/25/2022]
Abstract
MicroRNAs (miRNAs) are 21-25 nt long non-coding RNA that modulate various biological processes, including developmental timing via regulating the expression of their target genes. One critical determinant of normal postnatal lung architecture is septation, and there are many miRNAs involved in the development process. miR-134 is reported as a powerful inducer of pluripotent stem cell differentiation, and we have found that miR-134 is strongly downregulated during mice lung septation (from postnatal Day 2 to postnatal Day 21). Further cell function experiments have revealed that over-expression of miR-134 in A549 and Calu-3 cells can promote cell proliferation and inhibit cell apoptosis and migration abilities in vitro, and the down-expression of miR-134 in cells can act in the opposite way, which indicate that miR-134 is associated with lung septation. This study provides a basis for further investigation of its function in lung development.
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Affiliation(s)
- Xiaoying Zhang
- Department of Pediatrics, BaYi Children's Hospital of The General Military Hospital of Beijing PLA, Dongcheng District, Beijing, People's Republic of China.
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84
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Migliore C, Martin V, Leoni VP, Restivo A, Atzori L, Petrelli A, Isella C, Zorcolo L, Sarotto I, Casula G, Comoglio PM, Columbano A, Giordano S. MiR-1 downregulation cooperates with MACC1 in promoting MET overexpression in human colon cancer. Clin Cancer Res 2011; 18:737-47. [PMID: 22179665 DOI: 10.1158/1078-0432.ccr-11-1699] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE MET, the tyrosine kinase receptor for hepatocyte growth factor, is frequently overexpressed in colon cancers with high metastatic tendency. We aimed to evaluate the role of its negative regulators, miR-1 and miR-199a*, and its transcriptional activator, the metastasis-associated in colon cancer 1 (MACC1), in controlling MET expression in human colon cancer samples. EXPERIMENTAL DESIGN The expression of MET, miR-1, miR-199a*, and MACC1 was evaluated by real-time PCR in 52 matched pairs of colorectal cancers and nontumoral surrounding tissues. The biological role of miR-1 in controlling MET expression and biological activity was assessed in colon cancer cells either by its forced expression or by AntagomiR-mediated inhibition. RESULTS MiR-1 was downregulated in 84.6% of the tumors and its decrease significantly correlated with MET overexpression, particularly in metastatic tumors. We found that concurrent MACC1 upregulation and miR-1 downregulation are required to elicit the highest increase of MET expression. Consistent with a suppressive role of miR-1, its forced in vitro expression in colon cancer cells reduced MET levels and impaired MET-induced invasive growth. Finally, we identified a feedback loop between miR-1 and MET, resulting in their mutual regulation. CONCLUSIONS This study identifies an oncosuppressive role of miR-1 in colorectal cancer in which it acts by controlling MET expression through a feedback loop. Concomitant downregulation of miR-1 and increase of MACC1 can thus contribute to MET overexpression and to the metastatic behavior of colon cancer cells.
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Affiliation(s)
- Cristina Migliore
- IRCC, Institute for Cancer Research and Treatment, University of Torino School of Medicine, Candiolo, Turin, Italy
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85
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Qureshi IA, Mehler MF. Epigenetics, nervous system tumors, and cancer stem cells. Cancers (Basel) 2011; 3:3525-56. [PMID: 24212967 PMCID: PMC3759209 DOI: 10.3390/cancers3033525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/01/2011] [Accepted: 09/08/2011] [Indexed: 12/11/2022] Open
Abstract
Recent advances have begun to elucidate how epigenetic regulatory mechanisms are responsible for establishing and maintaining cell identity during development and adult life and how the disruption of these processes is, not surprisingly, one of the hallmarks of cancer. In this review, we describe the major epigenetic mechanisms (i.e., DNA methylation, histone and chromatin modification, non-coding RNA deployment, RNA editing, and nuclear reorganization) and discuss the broad spectrum of epigenetic alterations that have been uncovered in pediatric and adult nervous system tumors. We also highlight emerging evidence that suggests epigenetic deregulation is a characteristic feature of so-called cancer stem cells (CSCs), which are thought to be present in a range of nervous system tumors and responsible for tumor maintenance, progression, treatment resistance, and recurrence. We believe that better understanding how epigenetic mechanisms operate in neural cells and identifying the etiologies and consequences of epigenetic deregulation in tumor cells and CSCs, in particular, are likely to promote the development of enhanced molecular diagnostics and more targeted and effective therapeutic agents for treating recalcitrant nervous system tumors.
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Affiliation(s)
- Irfan A. Qureshi
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; E-Mail:
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Mark F. Mehler
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; E-Mail:
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-718-430-3543; Fax: +1-718-918-7505
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86
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Cullen BR. Viruses and microRNAs: RISCy interactions with serious consequences. Genes Dev 2011; 25:1881-94. [PMID: 21896651 DOI: 10.1101/gad.17352611] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Analyses of small RNA expression profiles have revealed that several DNA viruses-including particularly, herpesviruses-express high levels of multiple viral microRNAs (miRNAs) in infected cells. Here, I review our current understanding of how viral miRNAs influence viral replication and pathogenesis and discuss how viruses reshape the pattern of cellular miRNA expression. Indeed, viruses are now known to both activate and repress the expression of specific cellular miRNAs, and disrupting this process can perturb the ability of viruses to replicate normally. In addition, it is now clear that virally encoded miRNAs play a key role in inhibiting antiviral innate immune responses and can also promote cell transformation in culture. While our understanding of how viruses interact with miRNAs remains somewhat rudimentary, it is nevertheless already clear that these interactions can play a critical role in mediating viral pathogenesis and therefore may represent novel and highly specific targets for therapeutic intervention.
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Affiliation(s)
- Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
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87
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Verhagen APM, Pruijn GJM. Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity. Bioessays 2011; 33:674-82. [PMID: 21735459 DOI: 10.1002/bies.201100048] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 06/06/2011] [Accepted: 06/09/2011] [Indexed: 12/21/2022]
Abstract
Here we discuss the hypothesis that the RNA components of the Ro ribonucleoproteins (RNPs), the Y RNAs, can be processed into microRNAs (miRNAs). Although Ro RNPs, whose main protein components Ro60 and La are targeted by the immune system in several autoimmune diseases, were discovered many years ago, their function is still poorly understood. Indeed, recent data show that miRNA-sized small RNAs can be generated from Y RNAs. This hypothesis leads also to a model in which Ro60 acts as a modulator in the Y RNA-derived miRNA biogenesis pathway. The implications of these Y RNA-derived miRNAs, which may be specifically produced under pathological circumstances such as in autoimmunity or during viral infections, for the enigmatic function of Ro RNPs are discussed.
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Affiliation(s)
- Anja P M Verhagen
- Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands.
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88
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Abstract
Eukaryotic genomes accommodate numerous types of information within diverse DNA and RNA sequence elements. At many loci, these elements overlap and the same sequence is read multiple times during the production, processing, localization, function and turnover of a single transcript. Moreover, two or more transcripts from the same locus might use a common sequence in different ways, to perform distinct biological roles. Recent results show that many transcripts also undergo post-transcriptional cleavage to release specific fragments, which can then function independently. This phenomenon appears remarkably widespread, with even well-documented transcript classes such as messenger RNAs yielding fragments. RNA fragmentation significantly expands the already extraordinary spectrum of transcripts present within eukaryotic cells, and also calls into question how the 'gene' should be defined.
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89
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Bortoluzzi S, Biasiolo M, Bisognin A. MicroRNA-offset RNAs (moRNAs): by-product spectators or functional players? Trends Mol Med 2011; 17:473-4. [PMID: 21700497 DOI: 10.1016/j.molmed.2011.05.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/10/2011] [Accepted: 05/16/2011] [Indexed: 12/17/2022]
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90
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Qureshi IA, Mehler MF. Diagnosing and Treating Nervous System Disorders by Targeting Novel Classes of Non-coding RNAs. INTERNATIONAL DRUG DISCOVERY 2011; 6:30-36. [PMID: 26659096 PMCID: PMC4675140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Irfan A Qureshi
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine ; Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine ; Departments of Neurology, Albert Einstein College of Medicine ; Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine
| | - Mark F Mehler
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine ; Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine ; Departments of Neurology, Albert Einstein College of Medicine ; Neuroscience, Albert Einstein College of Medicine ; Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine ; Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine
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91
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Dhahbi JM, Atamna H, Boffelli D, Magis W, Spindler SR, Martin DIK. Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence. PLoS One 2011; 6:e20509. [PMID: 21637828 PMCID: PMC3102725 DOI: 10.1371/journal.pone.0020509] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/29/2011] [Indexed: 11/19/2022] Open
Abstract
In cell senescence, cultured cells cease proliferating and acquire aberrant gene expression patterns. MicroRNAs (miRNAs) modulate gene expression through translational repression or mRNA degradation and have been implicated in senescence. We used deep sequencing to carry out a comprehensive survey of miRNA expression and involvement in cell senescence. Informatic analysis of small RNA sequence datasets from young and senescent IMR90 human fibroblasts identifies many miRNAs that are regulated (either up or down) with cell senescence. Comparison with mRNA expression profiles reveals potential mRNA targets of these senescence-regulated miRNAs. The target mRNAs are enriched for genes involved in biological processes associated with cell senescence. This result greatly extends existing information on the role of miRNAs in cell senescence and is consistent with miRNAs having a causal role in the process.
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Affiliation(s)
- Joseph M. Dhahbi
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (JMD); (HA); (DIKM)
| | - Hani Atamna
- Department of Basic Sciences, Neuroscience, The Commonwealth Medical College, Scranton, Pennsylvania, United States of America
- * E-mail: (JMD); (HA); (DIKM)
| | - Dario Boffelli
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Wendy Magis
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Stephen R. Spindler
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
| | - David I. K. Martin
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- * E-mail: (JMD); (HA); (DIKM)
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92
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Kaya KD, Karakülah G, Yakicier CM, Acar AC, Konu O. mESAdb: microRNA expression and sequence analysis database. Nucleic Acids Res 2011; 39:D170-80. [PMID: 21177657 PMCID: PMC3013750 DOI: 10.1093/nar/gkq1256] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.
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Affiliation(s)
- Koray D Kaya
- Department of Molecular Biology and Genetics, Bilkent University, 06800 Ankara, Turkey
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93
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Findeiss S, Langenberger D, Stadler PF, Hoffmann S. Traces of post-transcriptional RNA modifications in deep sequencing data. Biol Chem 2011; 392:305-13. [PMID: 21345160 DOI: 10.1515/bc.2011.043] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many aspects of the RNA maturation leave traces in RNA sequencing data in the form of deviations from the reference genomic DNA. This includes, in particular, genomically non-encoded nucleotides and chemical modifications. The latter leave their signatures in the form of mismatches and conspicuous patterns of sequencing reads. Modified mapping procedures focusing on particular types of deviations can help to unravel post-transcriptional modification, maturation and degradation processes. Here, we focus on small RNA sequencing data that is produced in large quantities aimed at the analysis of microRNA expression. Starting from the recovery of many well known modified sites in tRNAs, we provide evidence that modified nucleotides are a pervasive phenomenon in these data sets. Regarding non-encoded nucleotides we concentrate on CCA tails, which surprisingly can be found in a diverse collection of transcripts including sub-populations of mature microRNAs. Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation.
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Affiliation(s)
- Sven Findeiss
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelsrtrasse 16-18, Leipzig, Germany
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94
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Langenberger D, Bartschat S, Hertel J, Hoffmann S, Tafer H, Stadler PF. MicroRNA or Not MicroRNA? ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2011. [DOI: 10.1007/978-3-642-22825-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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95
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Chakravarthy S, Sternberg SH, Kellenberger CA, Doudna JA. Substrate-specific kinetics of Dicer-catalyzed RNA processing. J Mol Biol 2010; 404:392-402. [PMID: 20932845 DOI: 10.1016/j.jmb.2010.09.030] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/07/2010] [Accepted: 09/14/2010] [Indexed: 12/21/2022]
Abstract
The specialized ribonuclease Dicer plays a central role in eukaryotic gene expression by producing small regulatory RNAs-microRNAs (miRNAs) and short interfering RNAs (siRNAs)-from larger double-stranded RNA (dsRNA) substrates. Although Dicer will cleave both imperfectly base-paired hairpin structures (pre-miRNAs) and perfect duplexes (pre-siRNAs) in vitro, it has not been clear whether these are mechanistically equivalent substrates and how dsRNA binding proteins such as trans-activation response (TAR) RNA binding protein (TRBP) influence substrate selection and RNA processing efficiency. We show here that human Dicer is much faster at processing a pre-miRNA substrate compared to a pre-siRNA substrate under both single and multiple turnover conditions. Maximal cleavage rates (V(max)) calculated by Michaelis-Menten analysis differed by more than 100-fold under multiple turnover conditions. TRBP was found to enhance dicing of both substrates to similar extents, and this stimulation required the two N-terminal dsRNA binding domains of TRBP. These results demonstrate that multiple factors influence dicing kinetics. While TRBP stimulates dicing by enhancing the stability of Dicer-substrate complexes, Dicer itself generates product RNAs at rates determined at least in part by the structural properties of the substrate.
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