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Soula A, Valere M, López-González MJ, Ury-Thiery V, Groppi A, Landry M, Nikolski M, Favereaux A. Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures. Life Sci Alliance 2018; 1:e201800018. [PMID: 30456375 PMCID: PMC6238413 DOI: 10.26508/lsa.201800018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022] Open
Abstract
Small RNA-Seq of the rat central nervous system reveals known and novel miRNAs specifically regulated in brain structures and correlated with the expression of their predicted target genes, suggesting a critical role in the transcriptomic identity of brain structures. In the central nervous system (CNS), miRNAs are involved in key functions, such as neurogenesis and synaptic plasticity. Moreover, they are essential to define specific transcriptomes in tissues and cells. However, few studies were performed to determine the miRNome of the different structures of the rat CNS, although a major model in neuroscience. Here, we determined by small RNA-Seq, the miRNome of the olfactory bulb, the hippocampus, the cortex, the striatum, and the spinal cord and showed the expression of 365 known miRNAs and 90 novel miRNAs. Differential expression analysis showed that several miRNAs were specifically enriched/depleted in these CNS structures. Transcriptome analysis by mRNA-Seq and correlation based on miRNA target predictions suggest that the specifically enriched/depleted miRNAs have a strong impact on the transcriptomic identity of the CNS structures. Altogether, these results suggest the critical role played by these enriched/depleted miRNAs, in particular the novel miRNAs, in the functional identities of CNS structures.
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Affiliation(s)
- Anaïs Soula
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Mélissa Valere
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - María-José López-González
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Vicky Ury-Thiery
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Alexis Groppi
- Centre de Bioinformatique de Bordeaux, University of Bordeaux, Bordeaux, France
| | - Marc Landry
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
| | - Macha Nikolski
- Centre de Bioinformatique de Bordeaux, University of Bordeaux, Bordeaux, France.,CNRS/Laboratoire Bordelais de Recherche en Informatique, University of Bordeaux, Talence, France
| | - Alexandre Favereaux
- University of Bordeaux, Bordeaux, France.,Centre Nationale de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5297, Interdisciplinary Institute of Neuroscience, Bordeaux, France
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Abstract
UNLABELLED The hippocampus (HPC) is known to play an important role in learning, a process dependent on synaptic plasticity; however, the molecular mechanisms underlying this are poorly understood. ΔFosB is a transcription factor that is induced throughout the brain by chronic exposure to drugs, stress, and variety of other stimuli and regulates synaptic plasticity and behavior in other brain regions, including the nucleus accumbens. We show here that ΔFosB is also induced in HPC CA1 and DG subfields by spatial learning and novel environmental exposure. The goal of the current study was to examine the role of ΔFosB in hippocampal-dependent learning and memory and the structural plasticity of HPC synapses. Using viral-mediated gene transfer to silence ΔFosB transcriptional activity by expressing ΔJunD (a negative modulator of ΔFosB transcriptional function) or to overexpress ΔFosB, we demonstrate that HPC ΔFosB regulates learning and memory. Specifically, ΔJunD expression in HPC impaired learning and memory on a battery of hippocampal-dependent tasks in mice. Similarly, general ΔFosB overexpression also impaired learning. ΔJunD expression in HPC did not affect anxiety or natural reward, but ΔFosB overexpression induced anxiogenic behaviors, suggesting that ΔFosB may mediate attentional gating in addition to learning. Finally, we found that overexpression of ΔFosB increases immature dendritic spines on CA1 pyramidal cells, whereas ΔJunD reduced the number of immature and mature spine types, indicating that ΔFosB may exert its behavioral effects through modulation of HPC synaptic function. Together, these results suggest collectively that ΔFosB plays a significant role in HPC cellular morphology and HPC-dependent learning and memory. SIGNIFICANCE STATEMENT Consolidation of our explicit memories occurs within the hippocampus, and it is in this brain region that the molecular and cellular processes of learning have been most closely studied. We know that connections between hippocampal neurons are formed, eliminated, enhanced, and weakened during learning, and we know that some stages of this process involve alterations in the transcription of specific genes. However, the specific transcription factors involved in this process are not fully understood. Here, we demonstrate that the transcription factor ΔFosB is induced in the hippocampus by learning, regulates the shape of hippocampal synapses, and is required for memory formation, opening up a host of new possibilities for hippocampal transcriptional regulation.
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Geller SF, Stone J. Quantitative PCR analysis of FosB mRNA expression after short duration oxygen and light stress. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2004; 533:249-57. [PMID: 15180271 DOI: 10.1007/978-1-4615-0067-4_31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Quantitative polymerase chain reaction (QPCR) was used to examine changes in FosB mRNA expression in models of oxygen and light stress to the retina. C57BL/6 mice or Sprague-Dawley (SD) albino rats were subjected to several experimental paradigms: short-term light or oxygen stress, extended hyperoxia (75% oxygen), or a model of oxygen-induced retinopathy (OIR). Control animals were subjected to room air and 5 lux cyclic light. FosB expression dramatically increases in response to light stress as well as in a model of OIR, but not in response to sustained 75% oxygen. These data suggest that both hypoxia and light stress induce expression of FosB in the retina.
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Affiliation(s)
- Scott F Geller
- School of Optometry, University of California, Berkeley, CA 94720-2020, USA.
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Criswell T, Leskov K, Miyamoto S, Luo G, Boothman DA. Transcription factors activated in mammalian cells after clinically relevant doses of ionizing radiation. Oncogene 2003; 22:5813-27. [PMID: 12947388 DOI: 10.1038/sj.onc.1206680] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Over the past 15 years, a wealth of information has been published on transcripts and proteins 'induced' (requiring new protein synthesis) in mammalian cells after ionizing radiation (IR) exposure. Many of these studies have also attempted to elucidate the transcription factors that are 'activated' (i.e., not requiring de novo synthesis) in specific cells by IR. Unfortunately, all too often this information has been obtained using supralethal doses of IR, with investigators assuming that induction of these proteins, or activation of corresponding transcription factors, can be 'extrapolated' to low-dose IR exposures. This review focuses on what is known at the molecular level about transcription factors induced at clinically relevant (< or =2 Gy) doses of IR. A review of the literature demonstrates that extrapolation from high doses of IR to low doses of IR is inaccurate for most transcription factors and most IR-inducible transcripts/proteins, and that induction of transactivating proteins at low doses must be empirically derived. The signal transduction pathways stimulated after high versus low doses of IR, which act to transactivate certain transcription factors in the cell, will be discussed. To date, only three transcription factors appear to be responsive (i.e. activated) after physiological doses (doses wherein cells survive or recover) of IR. These are p53, nuclear factor kappa B(NF-kappaB), and the SP1-related retinoblastoma control proteins (RCPs). Clearly, more information on transcription factors and proteins induced in mammalian cells at clinically or environmentally relevant doses of IR is needed to understand the role of these stress responses in cancer susceptibility/resistance and radio-sensitivity/resistance mechanisms.
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Affiliation(s)
- Tracy Criswell
- Department of Radiation Oncology and Program in Molecular Basis of Disease, Laboratory of Molecular Stress Responses, Ireland Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, OH 44106-4942, USA
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Hildesheim J, Kühn U, Yee CL, Foster RA, Yancey KB, Vogel JC. The hSkn-1a POU transcription factor enhances epidermal stratification by promoting keratinocyte proliferation. J Cell Sci 2001; 114:1913-23. [PMID: 11329378 DOI: 10.1242/jcs.114.10.1913] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Skn-1a is a POU transcription factor that is primarily expressed in the epidermis and is known to modulate the expression of several genes associated with keratinocyte differentiation. However, the formation of a stratified epidermis requires a carefully controlled balance between keratinocyte proliferation and differentiation, and a role for Skn-1a in this process has not been previously demonstrated. Here, our results show, surprisingly, that human Skn-1a contributes to epidermal stratification by primarily promoting keratinocyte proliferation and secondarily by enhancing the subsequent keratinocyte differentiation. In organotypic raft cultures of both primary human keratinocytes and immortalized HaCaT keratinocytes, human Skn-1a expression is associated with increased keratinocyte proliferation and re-epithelialization of the dermal substrates, resulting in increased numbers of keratinocytes available for the differentiation process. In these same raft cultures, human Skn-1a expression enhances the phenotypic changes of keratinocyte differentiation and the upregulated expression of keratinocyte differentiation genes. Conversely, expression of a dominant negative human Skn-1a transcription factor lacking the C-terminal transactivation domain blocks keratinocytes from proliferating and stratifying. Keratinocyte stratification is dependent on a precise balance between keratinocyte proliferation and differentiation, and our results suggest that human Skn-1a has an important role in maintaining epidermal homeostasis by promoting keratinocyte proliferation.
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Affiliation(s)
- J Hildesheim
- Dermatology Branch, National Cancer Institute, NIH, Building 10, Room 12N238, Bethesda, MD 20892-1908, USA
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Leonard AJ, Pickard MR, Sinha AK, Edwards PR, Evans IM, Ekins RP. SHORT COMMUNICATION maternal thyroid dysfunction and c- fos and c- jun expression in rat placenta. Placenta 1999; 20:727-31. [PMID: 10527828 DOI: 10.1053/plac.1999.0426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Maternal thyroid dysfunction is associated with perturbed fetal brain development and neurological deficits in adulthood in rat and human. To investigate whether these effects occur secondary to placental dysfunction, c- fos and c- jun expression in placenta from normal (euthyroid) and moderately hypothyroid rat dams were investigated by Northern hybridization analysis. In normal placenta, c- fos expression increased by 74 per cent between 16 and 21 days of gestation (dg) whereas c- jun expression declined by 46 per cent. Moderate maternal hypothyroidism depressed placental c- fos expression by 32 per cent at 19 dg, but elevated c- fos and c- jun expression by 139 and 86 per cent, respectively, at 21 dg. Maternal hypothyroidism may therefore induce c- fos/c- jun -related placental dysfunction, but only relatively late in gestation when fetal thyroid function is already established.
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Affiliation(s)
- A J Leonard
- Division of Molecular Endocrinology, UCL Medical School, Mortimer Street, London, W1N 8AA, UK
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Herdegen T, Leah JD. Inducible and constitutive transcription factors in the mammalian nervous system: control of gene expression by Jun, Fos and Krox, and CREB/ATF proteins. BRAIN RESEARCH. BRAIN RESEARCH REVIEWS 1998; 28:370-490. [PMID: 9858769 DOI: 10.1016/s0165-0173(98)00018-6] [Citation(s) in RCA: 1054] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This article reviews findings up to the end of 1997 about the inducible transcription factors (ITFs) c-Jun, JunB, JunD, c-Fos, FosB, Fra-1, Fra-2, Krox-20 (Egr-2) and Krox-24 (NGFI-A, Egr-1, Zif268); and the constitutive transcription factors (CTFs) CREB, CREM, ATF-2 and SRF as they pertain to gene expression in the mammalian nervous system. In the first part we consider basic facts about the expression and activity of these transcription factors: the organization of the encoding genes and their promoters, the second messenger cascades converging on their regulatory promoter sites, the control of their transcription, the binding to dimeric partners and to specific DNA sequences, their trans-activation potential, and their posttranslational modifications. In the second part we describe the expression and possible roles of these transcription factors in neural tissue: in the quiescent brain, during pre- and postnatal development, following sensory stimulation, nerve transection (axotomy), neurodegeneration and apoptosis, hypoxia-ischemia, generalized and limbic seizures, long-term potentiation and learning, drug dependence and withdrawal, and following stimulation by neurotransmitters, hormones and neurotrophins. We also describe their expression and possible roles in glial cells. Finally, we discuss the relevance of their expression for nervous system functioning under normal and patho-physiological conditions.
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Affiliation(s)
- T Herdegen
- Institute of Pharmacology, University of Kiel, Hospitalstrasse 4, 24105, Kiel,
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Abstract
Transcription factors function to regulate gene transcription. They may be constitutively expressed or may only be activated during specific situations. Activator protein-1 (AP-1) is an inducible transcription factor, and is comprised of multiple protein complexes that include the gene products of the fos and jun gene families. Numerous cellular and viral genes contain AP-1 binding sites within their promoters and, accordingly, AP-1 has been shown to play a role in the regulation of both basal and inducible transcription of these genes. fos-related antigen-2 (fra-2) has been found to have both similar and unique properties to that of other fos gene members in terms of its regulation and expression. The analysis and determination of the function of Fra-2 will provide further information on the role of AP-1.
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Affiliation(s)
- V C Foletta
- Division of Immunology and Cell Biology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Klintsova AY, Philpot BD, Brunjes PC. Fos protein immunoreactivity in the developing olfactory bulbs of normal and naris-occluded rats. BRAIN RESEARCH. DEVELOPMENTAL BRAIN RESEARCH 1995; 86:114-22. [PMID: 7656404 DOI: 10.1016/0165-3806(95)00015-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Immediate early genes such as c-fos may be a route through which extracellular events affect genomic expression. Expression of immediate early genes is important in the transcriptional regulation necessary for the normal development of the nervous system. Developmental patterns of Fos protein (the product of c-fos immediate early gene expression) were studied in the main olfactory bulb of the rat using immunocytochemistry. Embryonic Day 21 (E21, the last prenatal day), as well as Postnatal Day 0 (P0), P1, P5, P10, P15, P20 and P30 subjects were examined. Although staining was absent in the E21 bulb, there was a rapid onset of Fos synthesis within hours after birth. Distribution of Fos-immunoreactive (Fos-ir) nuclei corresponded to the sequence of bulb maturation: numerous mitral/tufted and granule cells were labeled on P0, followed by the appearance of Fos-ir in the nuclei of periglomerular cells and an increase in the number of stained granule cells with development. Surgical closure of an external naris on P1 resulted in a 70% reduction in the number of Fos-ir granule cell nuclei as early as 2 h after the manipulation. During the next 30 days, levels of Fos staining further diminished in experimental bulbs when compared to their contralateral controls. Nevertheless, electrical stimulation of the contralateral bulb in P20 pups resulted in a robust increase of Fos labeling in most main and accessory olfactory bulb mitral cells and in many granule and periglomerular neurons, suggesting that the experimental bulbs remain competent to express Fos protein.
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Affiliation(s)
- A Y Klintsova
- Department of Psychology, University of Virginia, Charlottesville 22903, USA
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Abstract
At the skin surface, the epidermis serves an important protective function which it manifests by building an extensive cytoskeletal architecture of keratin filaments, spanning from the nuclear envelope to hemidesmosomes and desmosomes. Recent studies on epidermal proteins and their interactions have provided insights into human skin diseases, including genetic disorders of keratins, laminins, and collagen. Explorations into the regulatory mechanisms underlying epidermal genes have underscored the importance of transcription factors AP-1 and AP-2, retinoic acid receptors, and POU proteins. Transgenic and gene ablation experiments on TGF-alpha and TGF-beta genes have yielded clues as to how the epidermis maintains a balance of growing and differentiating cells.
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Affiliation(s)
- E Fuchs
- Howard Hughes Medical Institute, Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637
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Wang SZ, Adler R. A developmentally regulated basic-leucine zipper-like gene and its expression in embryonic retina and lens. Proc Natl Acad Sci U S A 1994; 91:1351-5. [PMID: 8108415 PMCID: PMC43156 DOI: 10.1073/pnas.91.4.1351] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Transcriptional regulators play important roles in the control of key developmental events. We have identified sw3-3, a likely candidate for such a function, in tissues of the eye and other neural organs. It encodes a basic-leucine zipper-like protein, in which two leucine zipper motifs flank a basic domain. The latter contains helix-disturbing amino acids such as glycine and proline, at positions occupied by conserved asparagine and alanine residues (respectively) in "conventional" basic-leucine zipper proteins. sw3-3 is widely expressed at early embryonic stages in the lens, retina, and other neural tissues and is down-regulated thereafter with a spatial and temporal pattern that correlates with the cessation of mitotic activity and the onset of cell migration and differentiation.
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Affiliation(s)
- S Z Wang
- Retinal Degenerations Research Center, Wilmer Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21287-9257
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Grigoriadis AE, Schellander K, Wang ZQ, Wagner EF. Osteoblasts are target cells for transformation in c-fos transgenic mice. J Biophys Biochem Cytol 1993; 122:685-701. [PMID: 8335693 PMCID: PMC2119671 DOI: 10.1083/jcb.122.3.685] [Citation(s) in RCA: 275] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We have generated transgenic mice expressing the proto-oncogene c-fos from an H-2Kb class I MHC promoter as a tool to identify and isolate cell populations which are sensitive to altered levels of Fos protein. All homozygous H2-c-fosLTR mice develop osteosarcomas with a short latency period. This phenotype is specific for c-fos as transgenic mice expressing the fos- and jun-related genes, fosB and c-jun, from the same regulatory elements do not develop any pathology despite high expression in bone tissues. The c-fos transgene is not expressed during embryogenesis but is expressed after birth in bone tissues before the onset of tumor formation, specifically in putative preosteoblasts, bone-forming osteoblasts, osteocytes, as well as in osteoblastic cells present within the tumors. Primary and clonal cell lines established from c-fos-induced tumors expressed high levels of exogenous c-fos as well as the bone cell marker genes, type I collagen, alkaline phosphatase, and osteopontin/2ar. In contrast, osteocalcin/BGP expression was either low or absent. All cell lines were tumorigenic in vivo, some of which gave rise to osteosarcomas, expressing exogenous c-fos mRNA, and Fos protein in osteoblastic cells. Detailed analysis of one osteogenic cell line, P1, and several P1-derived clonal cell lines indicated that bone-forming osteoblastic cells were transformed by Fos. The regulation of osteocalcin/BGP and alkaline phosphatase gene expression by 1,25-dihydroxyvitamin D3 was abrogated in P1-derived clonal cells, whereas glucocorticoid responsiveness was unaltered. These results suggest that high levels of Fos perturb the normal growth control of osteoblastic cells and exert specific effects on the expression of the osteoblast phenotype.
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