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Koffler-Brill T, Noy Y, Avraham KB. The long and short: Non-coding RNAs in the mammalian inner ear. Hear Res 2023; 428:108666. [PMID: 36566643 PMCID: PMC9883734 DOI: 10.1016/j.heares.2022.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 10/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Non-coding RNAs (ncRNAs) play a critical role in the entire body, and their mis-regulation is often associated with disease. In parallel with the advances in high-throughput sequencing technologies, there is a great deal of focus on this broad class of RNAs. Although these molecules are not translated into proteins, they are now well established as significant regulatory components in many biological pathways and pathological conditions. ncRNAs can be roughly divided into two main sub-groups based on the length of the transcript, with both the small and long non-coding RNAs having diverse regulatory functions. The smaller length group includes ribosomal RNAs (rRNA), transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), microRNAs (miRNA), small interfering RNAs (siRNA), and PIWI-associated RNAs (piRNA). The longer length group includes linear long non-coding RNAs (lncRNA) and circular RNAs (circRNA). This review is designed to present the different classes of small and long ncRNA molecules and describe some of their known roles in physiological and pathological conditions, as well as methods used to assess the validity and function of miRNAs and lncRNAs, with a focus on their role and functions in the inner ear, hearing and deafness.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Noy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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2
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Abstract
Current estimates suggest that nearly half a billion people worldwide are affected by hearing loss. Because of the major psychological, social, economic, and health ramifications, considerable efforts have been invested in identifying the genes and molecular pathways involved in hearing loss, whether genetic or environmental, to promote prevention, improve rehabilitation, and develop therapeutics. Genomic sequencing technologies have led to the discovery of genes associated with hearing loss. Studies of the transcriptome and epigenome of the inner ear have characterized key regulators and pathways involved in the development of the inner ear and have paved the way for their use in regenerative medicine. In parallel, the immense preclinical success of using viral vectors for gene delivery in animal models of hearing loss has motivated the industry to work on translating such approaches into the clinic. Here, we review the recent advances in the genomics of auditory function and dysfunction, from patient diagnostics to epigenetics and gene therapy.
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Affiliation(s)
- Shahar Taiber
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; ,
| | - Kathleen Gwilliam
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA; ,
| | - Ronna Hertzano
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA; ,
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; ,
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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3
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Avraham KB, Khalaily L, Noy Y, Kamal L, Koffler-Brill T, Taiber S. The noncoding genome and hearing loss. Hum Genet 2022; 141:323-333. [PMID: 34491412 DOI: 10.1007/s00439-021-02359-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/29/2021] [Indexed: 12/16/2022]
Abstract
The age of sequencing has provided unprecedented insights into the human genome. The coding region of the genome comprises nearly 20,000 genes, of which approximately 4000 are associated with human disease. Beyond the protein-coding genome, which accounts for only 3% of the genome, lies a vast pool of regulatory elements in the form of promoters, enhancers, RNA species, and other intricate elements. These features undoubtably influence human health and disease, and as a result, a great deal of effort is currently being invested in deciphering their identity and mechanism. While a paucity of material has caused a lag in identifying these elements in the inner ear, the emergence of technologies for dealing with a minimal number of cells now has the field working overtime to catch up. Studies on microRNAs (miRNAs), long non-coding RNAs (lncRNAs), methylation, histone modifications, and more are ongoing. A number of microRNAs and other noncoding elements are known to be associated with hearing impairment and there is promise that regulatory elements will serve as future tools and targets of therapeutics and diagnostics. This review covers the current state of the field and considers future directions for the noncoding genome and implications for hearing loss.
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Affiliation(s)
- Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel.
| | - Lama Khalaily
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Yael Noy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Lara Kamal
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
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4
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Jiang X, Wang L, Xie S, Chen Y, Song S, Lu Y, Lu D. Long noncoding RNA MEG3 blocks telomerase activity in human liver cancer stem cells epigenetically. Stem Cell Res Ther 2020; 11:518. [PMID: 33256840 PMCID: PMC7706068 DOI: 10.1186/s13287-020-02036-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MEG3 downregulated the expression in several tumors and inhibits human tumorigenesis. But so far, the mechanism of MEG3 in tumorigenesis is still unclear. METHODS In gene infection, cellular and molecular technologies and tumorigenesis test in vitro and in vivo were performed, respectively. RESULTS Our results indicate that MEG3 enhances the P53 expression by triggering the loading of P300 and RNA polymerase II onto its promoter regions dependent on HP1α. Moreover, MEG3 increases the methylation modification of histone H3 at the 27th lysine via P53. Furthermore, MEG3 inhibits the expression of TERT by increasing the H3K27me3 in TERT promoter regions, thereby inhibiting the activity of telomerase by reducing the binding of TERT to TERC. Furthermore, MEG3 also increases the expression of TERRA; therefore, the interaction between TERC and TERT was competitively attenuated by increasing the interaction between TERRA and TERT, which inhibits the activity of telomerase in hLCSCs. Strikingly, MEG3 reduces the length of telomere by blocking the formation of complex maintaining telomere length (POT1-Exo1-TRF2-SNM1B) and decreasing the binding of the complex to telomere by increasing the interplay between P53 and HULC. Ultimately, MEG3 inhibits the growth of hLCSCs by reducing the activity of telomerase and attenuating telomeric repeat binding factor 2(TRF2). CONCLUSIONS Our results demonstrates MEG3 inhibits the occurrence of human liver cancer by blocking telomere, and these findings provide an important insight into the prevention and treatment of human liver cancer.
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Affiliation(s)
- Xiaoxue Jiang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Liyan Wang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Sijie Xie
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yingjie Chen
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Shuting Song
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yanan Lu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Dongdong Lu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.
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5
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Koffler-Brill T, Taiber S, Anaya A, Bordeynik-Cohen M, Rosen E, Kolla L, Messika-Gold N, Elkon R, Kelley MW, Ulitsky I, Avraham KB. Identification and characterization of key long non-coding RNAs in the mouse cochlea. RNA Biol 2020; 18:1160-1169. [PMID: 33131415 DOI: 10.1080/15476286.2020.1836456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The auditory system is a complex sensory network with an orchestrated multilayer regulatory programme governing its development and maintenance. Accumulating evidence has implicated long non-coding RNAs (lncRNAs) as important regulators in numerous systems, as well as in pathological pathways. However, their function in the auditory system has yet to be explored. Using a set of specific criteria, we selected four lncRNAs expressed in the mouse cochlea, which are conserved in the human transcriptome and are relevant for inner ear function. Bioinformatic characterization demonstrated a lack of coding potential and an absence of evolutionary conservation that represent properties commonly shared by their class members. RNAscope® analysis of the spatial and temporal expression profiles revealed specific localization to inner ear cells. Sub-cellular localization analysis presented a distinct pattern for each lncRNA and mouse tissue expression evaluation displayed a large variability in terms of level and location. Our findings establish the expression of specific lncRNAs in different cell types of the auditory system and present a potential pathway by which the lncRNA Gas5 acts in the inner ear. Studying lncRNAs and deciphering their functions may deepen our knowledge of inner ear physiology and morphology and may reveal the basis of as yet unresolved genetic hearing loss-related pathologies. Moreover, our experimental design may be employed as a reference for studying other inner ear-related lncRNAs, as well as lncRNAs expressed in other sensory systems.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Anaya
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Einat Rosen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Likhitha Kolla
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Naama Messika-Gold
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Matthew W Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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6
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The molecular mechanisms of LncRNA-correlated PKM2 in cancer metabolism. Biosci Rep 2019; 39:220807. [PMID: 31654067 PMCID: PMC6851521 DOI: 10.1042/bsr20192453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/17/2022] Open
Abstract
Reprogrammed metabolism is an important hallmark of cancer cells. Pyruvate kinase (PK) is one of the major rate-limiting enzymes in glucose metabolism. The M2 isoform of PK (PKM2), is considered to be an important marker of metabolic reprogramming and one of the key enzymes. Recently, through the continuous development of genome-wide analysis and functional studies, accumulating evidence has demonstrated that long non-coding RNAs (LncRNAs) play vital regulatory roles in cancer progression by acting as either potential oncogenes or tumor suppressors. Furthermore, several studies have shown that up-regulation of PKM2 in cancer tissues is associated with LncRNAs expression and patient survival. Thus, scientists have begun to unveil the mechanism of LncRNA-associated PKM2 in cancer metabolic progression. Based on these novel findings, in this mini-review, we summarize the detailed molecular mechanisms of LncRNA related to PKM2 in cancer metabolism. We expect that this work will promote a better understanding of the molecular mechanisms of PKM2, and provide a profound potential for targeting PKM2 to treat tumors.
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7
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Xing Y, Zheng X, Fu Y, Qi J, Li M, Ma M, Wang S, Li S, Zhu D. Long Noncoding RNA-Maternally Expressed Gene 3 Contributes to Hypoxic Pulmonary Hypertension. Mol Ther 2019; 27:2166-2181. [PMID: 31477557 DOI: 10.1016/j.ymthe.2019.07.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 07/04/2019] [Accepted: 07/26/2019] [Indexed: 01/22/2023] Open
Abstract
The expression and function of long noncoding RNAs (lncRNAs) in the development of hypoxic pulmonary hypertension (HPH), especially in the proliferation of pulmonary artery smooth muscle cells (PASMCs), are largely unknown. Herein, we examined the expression and role of lncRNA-maternally expressed gene 3 (lncRNA-MEG3) in HPH. lncRNA-MEG3 was significantly increased and primarily localized in the cytoplasm of hypoxic PASMCs. lncRNA-MEG3 knockdown by lung-specific delivery of small interfering RNAs (siRNAs) significantly inhibited the development of HPH in vivo. Silencing of lncRNA-MEG3 by siRNAs and gapmers attenuated proliferation and cell-cycle progression in both PASMCs from idiopathic pulmonary arterial hypertension (iPAH) patients (iPAH-PASMCs) and hypoxia-exposed PASMCs in vitro. Mechanistically, we found that lncRNA-MEG3 interacts with and leads to the degradation of microRNA-328-3p (miR-328-3p), leading to upregulation of insulin-like growth factor 1 receptor (IGF1R). Additionally, higher expression of lncRNA-MEG3 and IGF1R and lower expression of miR-328-3p were observed in iPAH-PASMCs and relevant HPH models. These data provide insights into the contribution of lncRNA-MEG3 to HPH. Upregulation of lncRNA-MEG3 sequesters cytoplasmic miR-328-3p, eventually leading to expression of IGF1R, revealing a regulatory mechanism by lncRNAs in hypoxia-induced PASMC proliferation.
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Affiliation(s)
- Yan Xing
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang 163319, P.R. China
| | - Xiaodong Zheng
- Department of Genetics and Cell Biology, Harbin Medical University-Daqing, Daqing, Heilongjiang 163319, P.R. China.
| | - Yao Fu
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China
| | - Jing Qi
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China; Department of Pharmaceutical, Harbin Medical University-Daqing, Daqing, Heilongjiang 163319, P.R. China
| | - Minghui Li
- Department of Pharmaceutical, Harbin Medical University-Daqing, Daqing, Heilongjiang 163319, P.R. China
| | - Mingfei Ma
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China
| | - Shuang Wang
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Shuzhen Li
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Daling Zhu
- College of Pharmacy, Harbin Medical University, Harbin, 150081, P.R. China; Central Laboratory of Harbin Medical University-Daqing, Daqing 163319, P.R. China; State Province Key Laboratories of Biomedicine-Pharmaceutics of China, Daqing 163319, P.R. China; Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, Harbin, 150081, P.R. China.
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8
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Ushakov K, Koffler-Brill T, Rom A, Perl K, Ulitsky I, Avraham KB. Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems. Sci Rep 2017; 7:8637. [PMID: 28819115 PMCID: PMC5561060 DOI: 10.1038/s41598-017-08320-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction. To help address this need, we performed a whole-genome identification of lncRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 3,239 lncRNA genes, most of which were intergenic (lincRNAs) and 721 are novel. We examined temporal and tissue specificity by analyzing the developmental profiles on embryonic day 16.5 and at birth. The spatial and temporal patterns of three lncRNAs, two of which are in proximity to genes associated with hearing and deafness, were explored further. Our findings indicate that lncRNAs are prevalent in the sensory epithelium of the mouse inner ear and are likely to play key roles in regulating critical pathways for hearing and balance.
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Affiliation(s)
- Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Kobi Perl
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.,Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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9
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Doetzlhofer A, Avraham KB. Insights into inner ear-specific gene regulation: Epigenetics and non-coding RNAs in inner ear development and regeneration. Semin Cell Dev Biol 2016; 65:69-79. [PMID: 27836639 DOI: 10.1016/j.semcdb.2016.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/14/2016] [Accepted: 11/03/2016] [Indexed: 12/12/2022]
Abstract
The vertebrate inner ear houses highly specialized sensory organs, tuned to detect and encode sound, head motion and gravity. Gene expression programs under the control of transcription factors orchestrate the formation and specialization of the non-sensory inner ear labyrinth and its sensory constituents. More recently, epigenetic factors and non-coding RNAs emerged as an additional layer of gene regulation, both in inner ear development and disease. In this review, we provide an overview on how epigenetic modifications and non-coding RNAs, in particular microRNAs (miRNAs), influence gene expression and summarize recent discoveries that highlight their critical role in the proper formation of the inner ear labyrinth and its sensory organs. Finally, we discuss recent insights into how epigenetic factors and miRNAs may facilitate, or in the case of mammals, restrict inner ear sensory hair cell regeneration.
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Affiliation(s)
- Angelika Doetzlhofer
- The Solomon H. Snyder Department of Neuroscience, the Center for Sensory Biology, the Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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10
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Schrauwen I, Hasin-Brumshtein Y, Corneveaux JJ, Ohmen J, White C, Allen AN, Lusis AJ, Van Camp G, Huentelman MJ, Friedman RA. A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear. Hear Res 2015; 333:266-274. [PMID: 26341477 DOI: 10.1016/j.heares.2015.08.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 08/12/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://www.tgen.org/home/research/research-divisions/neurogenomics/supplementary-data/inner-ear-transcriptome.aspx.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium.,Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Yehudit Hasin-Brumshtein
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jason J Corneveaux
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Jeffrey Ohmen
- House Ear Institute, Los Angeles 90057, CA, United States
| | - Cory White
- House Ear Institute, Los Angeles 90057, CA, United States.,Keck School of Medicine, USC, Los Angeles, CA, United States
| | - April N Allen
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Rick A Friedman
- Keck School of Medicine, USC, Los Angeles, CA, United States
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11
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Sun Y, Liu PY, Scarlett CJ, Malyukova A, Liu B, Marshall GM, MacKenzie KL, Biankin AV, Liu T. Histone deacetylase 5 blocks neuroblastoma cell differentiation by interacting with N-Myc. Oncogene 2014; 33:2987-94. [PMID: 23812427 DOI: 10.1038/onc.2013.253] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/10/2013] [Accepted: 05/31/2013] [Indexed: 12/18/2022]
Abstract
The N-Myc oncoprotein induces neuroblastoma, which arises from undifferentiated neuroblasts in the sympathetic nervous system, by modulating gene and protein expression and consequently causing cell differentiation block and cell proliferation. The class IIa histone deacetylase 5 (HDAC5) represses gene transcription, and blocks myoblast, osteoblast and leukemia cell differentiation. Here we showed that N-Myc upregulated HDAC5 expression in neuroblastoma cells. Conversely, HDAC5 repressed the ubiquitin-protein ligase NEDD4 gene expression, increased Aurora A gene expression and consequently upregulated N-Myc protein expression. Genome-wide gene expression analysis and protein co-immunoprecipitation assays revealed that HDAC5 and N-Myc repressed the expression of a common subset of genes by forming a protein complex, whereas HDAC5 and the class III HDAC SIRT2 independently repressed the expression of another common subset of genes without forming a protein complex. Moreover, HDAC5 blocked differentiation and induced proliferation in neuroblastoma cells. Taken together, our data identify HDAC5 as a novel co-factor in N-Myc oncogenesis, and provide the evidence for the potential application of HDAC5 inhibitors in the therapy of N-Myc-induced neuroblastoma and potentially other c-Myc-induced malignancies.
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Affiliation(s)
- Y Sun
- Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia
| | - P Y Liu
- Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia
| | - C J Scarlett
- 1] School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia [2] Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - A Malyukova
- Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia
| | - B Liu
- 1] Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia [2] Kids Cancer Alliance, Randwick, New South Wales, Australia
| | - G M Marshall
- 1] Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia [2] Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - K L MacKenzie
- Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia
| | - A V Biankin
- 1] Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia [2] Department of Surgery, Bankstown Hospital, Bankstown, New South Wales, Australia [3] South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales, Australia
| | - T Liu
- 1] Children's Cancer Institute Australia for Medical Research, Randwick, New South Wales, Australia [2] School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, New South Wales, Australia
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Ushakov K, Rudnicki A, Avraham KB. MicroRNAs in sensorineural diseases of the ear. Front Mol Neurosci 2013; 6:52. [PMID: 24391537 PMCID: PMC3870287 DOI: 10.3389/fnmol.2013.00052] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/04/2013] [Indexed: 12/30/2022] Open
Abstract
Non-coding microRNAs (miRNAs) have a fundamental role in gene regulation and expression in almost every multicellular organism. Only discovered in the last decade, miRNAs are already known to play a leading role in many aspects of disease. In the vertebrate inner ear, miRNAs are essential for controlling development and survival of hair cells. Moreover, dysregulation of miRNAs has been implicated in sensorineural hearing impairment, as well as in other ear diseases such as cholesteatomas, vestibular schwannomas, and otitis media. Due to the inaccessibility of the ear in humans, animal models have provided the optimal tools to study miRNA expression and function, in particular mice and zebrafish. A major focus of current research has been to discover the targets of the miRNAs expressed in the inner ear, in order to determine the regulatory pathways of the auditory and vestibular systems. The potential for miRNAs manipulation in development of therapeutic tools for hearing impairment is as yet unexplored, paving the way for future work in the field.
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Affiliation(s)
- Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Anya Rudnicki
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
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Miller KA, Williams LH, Dahl HHM, Manji SSM. Eeyore: a novel mouse model of hereditary deafness. PLoS One 2013; 8:e74243. [PMID: 24086324 PMCID: PMC3781070 DOI: 10.1371/journal.pone.0074243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/31/2013] [Indexed: 11/18/2022] Open
Abstract
Animal models that recapitulate human disease are proving to be an invaluable tool in the identification of novel disease-associated genes. These models can improve our understanding of the complex genetic mechanisms involved in disease and provide a basis to guide therapeutic strategies to combat these conditions. We have identified a novel mouse model of non-syndromic sensorineural hearing loss with linkage to a region on chromosome 18. Eeyore mutant mice have early onset progressive hearing impairment and show abnormal structure of the sensory epithelium from as early as 4 weeks of age. Ultrastructural and histological analyses show irregular hair cell structure and degeneration of the sensory hair bundles in the cochlea. The identification of new genes involved in hearing is central to understanding the complex genetic pathways involved in the hearing process and the loci at which these pathways are interrupted in people with a genetic hearing loss. We therefore discuss possible candidate genes within the linkage region identified in eeyore that may underlie the deafness phenotype in these mice. Eeyore provides a new model of hereditary sensorineural deafness and will be an important tool in the search for novel deafness genes.
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Affiliation(s)
- Kerry A. Miller
- Genetic Hearing Research, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- * E-mail:
| | - Louise H. Williams
- Genetic Hearing Research, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Hans-Henrik M. Dahl
- Genetic Hearing Research, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- The HEARing CRC, Audiology, Hearing and Speech Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Shehnaaz S. M. Manji
- Genetic Hearing Research, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- The HEARing CRC, Audiology, Hearing and Speech Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Department of Otolaryngology, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
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Miller KA, Williams LH, Rose E, Kuiper M, Dahl HHM, Manji SSM. Inner ear morphology is perturbed in two novel mouse models of recessive deafness. PLoS One 2012; 7:e51284. [PMID: 23251483 PMCID: PMC3520982 DOI: 10.1371/journal.pone.0051284] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/31/2012] [Indexed: 11/29/2022] Open
Abstract
Human MYO7A mutations can cause a variety of conditions involving the inner ear. These include dominant and recessive non-syndromic hearing loss and syndromic conditions such as Usher syndrome. Mouse models of deafness allow us to investigate functional pathways involved in normal and abnormal hearing processes. We present two novel mouse models with mutations in the Myo7a gene with distinct phenotypes. The mutation in Myo7aI487N/I487N ewaso is located within the head motor domain of Myo7a. Mice exhibit a profound hearing loss and manifest behaviour associated with a vestibular defect. A mutation located in the linker region between the coiled-coil and the first MyTH4 domains of the protein is responsible in Myo7aF947I/F947I dumbo. These mice show a less severe hearing loss than in Myo7aI487N/I487N ewaso; their hearing loss threshold is elevated at 4 weeks old, and progressively worsens with age. These mice show no obvious signs of vestibular dysfunction, although scanning electron microscopy reveals a mild phenotype in vestibular stereocilia bundles. The Myo7aF947I/F947I dumbo strain is therefore the first reported Myo7a mouse model without an overt vestibular phenotype; a possible model for human DFNB2 deafness. Understanding the molecular basis of these newly identified mutations will provide knowledge into the complex genetic pathways involved in the maintenance of hearing, and will provide insight into recessively inherited sensorineural hearing loss in humans.
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Affiliation(s)
- Kerry A Miller
- Genetic Hearing Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.
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Johnson R, Noble W, Tartaglia GG, Buckley NJ. Neurodegeneration as an RNA disorder. Prog Neurobiol 2012; 99:293-315. [PMID: 23063563 PMCID: PMC7116994 DOI: 10.1016/j.pneurobio.2012.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/14/2012] [Accepted: 09/26/2012] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases constitute one of the single most important public health challenges of the coming decades, and yet we presently have only a limited understanding of the underlying genetic, cellular and molecular causes. As a result, no effective disease-modifying therapies are currently available, and no method exists to allow detection at early disease stages, and as a result diagnoses are only made decades after disease pathogenesis, by which time the majority of physical damage has already occurred. Since the sequencing of the human genome, we have come to appreciate that the transcriptional output of the human genome is extremely rich in non-protein coding RNAs (ncRNAs). This heterogeneous class of transcripts is widely expressed in the nervous system, and is likely to play many crucial roles in the development and functioning of this organ. Most exciting, evidence has recently been presented that ncRNAs play central, but hitherto unappreciated roles in neurodegenerative processes. Here, we review the diverse available evidence demonstrating involvement of ncRNAs in neurodegenerative diseases, and discuss their possible implications in the development of therapies and biomarkers for these conditions.
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Key Words
- neurodegeneration
- neurodegenerative disease
- non-coding rna
- alzheimer's disease
- parkinson's disease
- huntington's disease
- trinucleotide repeat disorder
- bace1
- rest
- long non-coding rna
- microrna
- har1
- sox2ot
- mir-9
- mir-132
- mir-124
- ndds, neurodegenerative disorders
- ad, alzheimer's disease
- hd, huntington's disease
- pd, parkinson's disease
- als, amyotrophic lateral sclerosis
- app, amyloid precursor protein
- cftr, cystic fibrosis
- csf, cerebrospinal fluid
- sod1, superoxide dismutase 1
- tardbp, tar dna binding protein
- psen-1, presenilin 1
- psen-2, presenilin 1
- mapt, microtubule-associated protein tau
- snca, α-synuclein
- ups, ubiquitin-proteasome system
- aββ, -amyloid
- er, endoplasmic reticulum
- ber, base excision repair
- parp-1, poly-adp ribose polymerase-1
- lncrnas, long non-coding rnas
- mirnas, microrna
- ncrna, non-coding rnas
- ngs, next generation sequencing
- pcr, polymerase chain reaction
- sars, severe acute respiratory disorder
- sca, spinal cerebellar ataxia
- dm, myotonic dystrophy
- hdl2, huntington's disease-like 2
- tnds, trinucleotide repeat disorders
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Affiliation(s)
- Rory Johnson
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Catalunya, Spain
| | - Wendy Noble
- Kings College London, Institute of Psychiatry, London, UK
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Catalunya, Spain
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Manji SSM, Miller KA, Williams LH, Dahl HHM. Identification of three novel hearing loss mouse strains with mutations in the Tmc1 gene. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 180:1560-9. [PMID: 22330676 DOI: 10.1016/j.ajpath.2011.12.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 12/11/2011] [Accepted: 12/22/2011] [Indexed: 11/25/2022]
Abstract
We report the identification of three new mouse models, baringo, nice, and stitch, with recessively inherited sensorineural deafness due to novel mutations in the transmembrane channel-like gene 1 (Tmc1). These strains were generated by N-ethyl-N-nitrosourea mutagenesis. DNA sequence analysis revealed changes in c.545A>G, c.1345T>C, and c.1661G>T, causing p.Y182C, p.Y449H, and p.W554L amino acid substitutions in baringo, nice, and stitch mutants, respectively. The mutations affect amino acid residues that are evolutionarily conserved across species. Similar to the previously reported Beethoven Tmc1 mutant, both p.Y182C and p.W554L are located outside a predicted transmembrane domain, whereas the p.Y449H mutation resides in the predicted transmembrane domain 4. Homozygous stitch-mutant mice have severe hearing loss at the age of 4 weeks and are deaf by the age of 8 weeks, whereas both baringo and nice mutants are profoundly deaf at the age of 4 weeks. None of the strains displays signs of vestibular dysfunction. Scanning electron microscopy revealed degeneration of outer hair cells in the basal region of baringo, nice, and stitch mutants. Immunolocalization studies revealed expression of TMC1 protein in the hair cells, spiral ganglion neurons, supporting cells, and stria ligament in the inner ear. Reduced levels of TMC1 protein were observed in the spiral ligament of mutants when compared with wild-type animals. These three allelic mutants provide valuable models for studying nonsyndromic recessive sensorineural hearing loss (DFNB7/11) in humans.
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Affiliation(s)
- Shehnaaz S M Manji
- Genetic Hearing Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia.
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Neurotrophic receptors as potential therapy targets in postnatal development, in adult, and in hearing loss-affected inner ear. Otol Neurotol 2011; 32:761-73. [PMID: 21646930 DOI: 10.1097/mao.0b013e31821f7cc1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
HYPOTHESIS The aim of this investigation was to define the expression of neurotrophic receptors within the developing inner ear of different postnatal ages. BACKGROUND Pattern of differential expression of neurotrophic receptors provide molecular target sites for multifunctional nanoparticle-based cell-specific therapeutics delivery to treat hearing diseases. METHODS Protein expression of neurotrophic receptors was studied by immune-histochemistry, quantitative polymerase chain reaction, in situ hybridization, Western blot, in early and late postnatal, adult, and aging mice. RESULTS There was a high correlation between results obtained at ribonucleic acid and protein levels. TrkB and TrkC gene expression increased during the first 2 weeks and also after the onset of hearing in adult mice. At the onset of hearing, TrkB-immunopositive staining occurred in inner hair cells and in cell bodies of spiral ganglion neurons. TrkC was detected in nerve endings beneath inner and outer hair cells and in supporting cells. Root cells within the spiral ligament and spiral ganglion neurons in the Rosenthal's canal showed high level of TrkC expression. p75NTR was found in organ of Corti similar to TrkC, and scattered neurons showed strong immunoreactivity in the Rosenthal's canal. PD540 mice, a model of age-related hearing loss, showed a complete spiral ganglion cell loss in the basal turn. Although TrkB and TrkC were completely lacking in this region of the Rosenthal's canal, remaining nerve fibers were p75NTR immunopositive. CONCLUSION We found differential expression pattern of TrkB, TrkC, and p75NTR receptors in the inner ear and could make a receptor expression data base. These findings, in turn, will help to design a study on receptor-specific drug targeting of the mice model of auditory development and aging.
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Identification and analysis of intermediate size noncoding RNAs in the human fetal brain. PLoS One 2011; 6:e21652. [PMID: 21789175 PMCID: PMC3138756 DOI: 10.1371/journal.pone.0021652] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Accepted: 06/07/2011] [Indexed: 12/18/2022] Open
Abstract
The involvement of noncoding RNAs (ncRNAs) in the development of the human brain remains largely unknown. Applying a cloning strategy for detection of intermediate size (50–500 nt) ncRNAs (is-ncRNAs) we have identified 82 novel transcripts in human fetal brain tissue. Most of the novel is-ncRNAs are not well conserved in vertebrates, and several transcripts were only found in primates. Northern blot and microarray analysis indicated considerable variation in expression across human fetal brain development stages and fetal tissues for both novel and known is-ncRNAs. Expression of several of the novel is-ncRNAs was conspicuously absent in one or two brain cancer cell lines, and transient overexpression of some transcripts in cancer cells significantly inhibited cell proliferation. Overall, our results suggest that is-ncRNAs play important roles in the development and tumorigenesis of human brain.
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Cell-specific targeting in the mouse inner ear using nanoparticles conjugated with a neurotrophin-derived peptide ligand: potential tool for drug delivery. Int J Pharm 2010; 390:214-24. [PMID: 20153412 DOI: 10.1016/j.ijpharm.2010.02.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 02/03/2010] [Accepted: 02/04/2010] [Indexed: 01/19/2023]
Abstract
Cell specific targeting is an emerging field in nanomedicine. Homing of the multifunctional nanoparticles (MFNPs) is achieved by the conjugation of targeting moieties on the nanoparticle surface. The inner ear is an attractive target for new drug delivery strategies as it is hard to access and hearing loss is a significant worldwide problem. In this work we investigated the utility of a Nerve Growth Factor-derived peptide (hNgf_EE) functionalized nanoparticles (NPs) to target cells of the inner ear. These functionalized NPs were introduced to organotypic explant cultures of the mouse inner ear and to PC-12 rat pheochromocytoma cells. The NPs did not show any signs of toxicity. Specific targeting and higher binding affinity to spiral ganglion neurons, Schwann cells and nerve fibers of the explant cultures were achieved through ligand mediated multivalent binding to tyrosine kinase receptors and to p75 neurotrophin receptors. Unspecific uptake of NPs was investigated using NPs conjugated with scrambled hNgf_EE peptide. Our results indicate a selective cochlear cell targeting by MFNPs, which may be a potential tool for cell specific drug and gene delivery to the inner ear.
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Abstract
Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.
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