101
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Picardi E, Horner DS, Pesole G. Single-cell transcriptomics reveals specific RNA editing signatures in the human brain. RNA (NEW YORK, N.Y.) 2017; 23:860-865. [PMID: 28258159 PMCID: PMC5435858 DOI: 10.1261/rna.058271.116] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 02/21/2017] [Indexed: 06/02/2023]
Abstract
While RNA editing by A-to-I deamination is a requisite for neuronal function in humans, it is under-investigated in single cells. Here we fill this gap by analyzing RNA editing profiles of single cells from the brain cortex of living human subjects. We show that RNA editing levels per cell are bimodally distributed and distinguish between major brain cell types, thus providing new insights into neuronal dynamics.
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Affiliation(s)
- Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
- Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
- Institute of Biomembranes and Bioenergetics, National Research Council, 70126 Bari, Italy
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102
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Gal-Mark N, Shallev L, Sweetat S, Barak M, Billy Li J, Levanon EY, Eisenberg E, Behar O. Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition. Sci Rep 2017; 7:43421. [PMID: 28266523 PMCID: PMC5339895 DOI: 10.1038/srep43421] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/24/2017] [Indexed: 11/10/2022] Open
Abstract
Adenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level. A-to-I RNA editing is abundant in the brain, and altered editing levels have been reported in various neurological pathologies and following spinal cord injury (SCI). The prevailing concept is that the RNA editing process itself is dysregulated by brain pathologies. Here we analyzed recent RNA-seq data, and found that, except for few mammalian conserved editing sites, editing is significantly higher in neurons than in other cell populations of the brain. We studied A-to-I RNA editing in stab wound injury (SWI) and SCI models and showed that the apparent under-editing observed after injury correlates with an approximately 20% reduction in the relative density of neurons, due to cell death and immune cell infiltration that may account for the observed under-editing. Studies of neuronal and astrocyte cultures and a computational analysis of SCI RNA-seq data further supported the possibility that a reduction in neuronal density is responsible for alterations in the tissue-wide editing patterns upon injury. Thus, our data suggest that the case for a mechanistic linkage between A-to-I RNA editing and brain pathologies should be revisited.
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Affiliation(s)
- Nurit Gal-Mark
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lea Shallev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Sahar Sweetat
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Michal Barak
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oded Behar
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
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103
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Behm M, Wahlstedt H, Widmark A, Eriksson M, Öhman M. Accumulation of nuclear ADAR2 regulates adenosine-to-inosine RNA editing during neuronal development. J Cell Sci 2017; 130:745-753. [PMID: 28082424 DOI: 10.1242/jcs.200055] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/30/2016] [Indexed: 12/16/2022] Open
Abstract
Adenosine to inosine (A-to-I) RNA editing is important for a functional brain, and most known sites that are subject to selective RNA editing have been found to result in diversified protein isoforms that are involved in neurotransmission. In the absence of the active editing enzymes ADAR1 or ADAR2 (also known as ADAR and ADARB1, respectively), mice fail to survive until adulthood. Nuclear A-to-I editing of neuronal transcripts is regulated during brain development, with low levels of editing in the embryo and a dramatic increase after birth. Yet, little is known about the mechanisms that regulate editing during development. Here, we demonstrate lower levels of ADAR2 in the nucleus of immature neurons than in mature neurons. We show that importin-α4 (encoded by Kpna3), which increases during neuronal maturation, interacts with ADAR2 and contributes to the editing efficiency by bringing it into the nucleus. Moreover, we detect an increased number of interactions between ADAR2 and the nuclear isomerase Pin1 as neurons mature, which contribute to ADAR2 protein stability. Together, these findings explain how the nuclear editing of substrates that are important for neuronal function can increase as the brain develops.
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Affiliation(s)
- Mikaela Behm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Helene Wahlstedt
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Albin Widmark
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Maria Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
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104
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Filippini A, Bonini D, La Via L, Barbon A. The Good and the Bad of Glutamate Receptor RNA Editing. Mol Neurobiol 2016; 54:6795-6805. [DOI: 10.1007/s12035-016-0201-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/11/2016] [Indexed: 12/15/2022]
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105
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Ramaswami G, Li JB. Identification of human RNA editing sites: A historical perspective. Methods 2016; 107:42-7. [PMID: 27208508 PMCID: PMC5014717 DOI: 10.1016/j.ymeth.2016.05.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 12/18/2022] Open
Abstract
A-to-I RNA editing is an essential gene regulatory mechanism. Once thought to be a rare phenomenon only occurring in a few transcripts, the emergence of high-throughput RNA sequencing has facilitated the identification of over 2 million RNA editing sites in the human transcriptome. In this review, we survey the current RNA-seq based methods as well as historical methods used to identify RNA editing sites.
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Affiliation(s)
- Gokul Ramaswami
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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106
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Larriba E, del Mazo J. Role of Non-Coding RNAs in the Transgenerational Epigenetic Transmission of the Effects of Reprotoxicants. Int J Mol Sci 2016; 17:452. [PMID: 27023531 PMCID: PMC4848908 DOI: 10.3390/ijms17040452] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are regulatory elements of gene expression and chromatin structure. Both long and small ncRNAs can also act as inductors and targets of epigenetic programs. Epigenetic patterns can be transmitted from one cell to the daughter cell, but, importantly, also through generations. Diversity of ncRNAs is emerging with new and surprising roles. Functional interactions among ncRNAs and between specific ncRNAs and structural elements of the chromatin are drawing a complex landscape. In this scenario, epigenetic changes induced by environmental stressors, including reprotoxicants, can explain some transgenerationally-transmitted phenotypes in non-Mendelian ways. In this review, we analyze mechanisms of action of reprotoxicants upon different types of ncRNAs and epigenetic modifications causing transgenerationally transmitted characters through germ cells but affecting germ cells and reproductive systems. A functional model of epigenetic mechanisms of transgenerational transmission ncRNAs-mediated is also proposed.
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Affiliation(s)
- Eduardo Larriba
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain.
| | - Jesús del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain.
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