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Vetrivel S, Truong DJJ, Wurst W, Graw J, Giesert F. Identification of ocular regulatory functions of core histone variant H3.2. Exp Eye Res 2023; 226:109346. [PMID: 36529279 DOI: 10.1016/j.exer.2022.109346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/05/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The posttranscriptional modifications (PTM) of the Histone H3 family play an important role in ocular system differentiation. However, there has been no study on the nature of specific Histone H3 subtype carrying these modifications. Fortuitously, we had previously identified a dominant small-eye mutant Aey69 mouse with a mutation in the H3.2 encoding Hist2h3c1 gene (Vetrivel et al., 2019). In continuation, in the present study, the role of Histone H3.2 with relation to the microphtalmic Aey69 has been elaborated. Foremost, a transgenic mouse line expressing the fusion protein H3.2-GFP was generated using Crispr/Cas9. The approach was intended to confer a unique tag to the Hist2h3c1 gene which is similar in sequence and encoded protein structure to other histones. The GFP tag was then used for ChIP Seq analysis of the genes regulated by H3.2. The approach revealed ocular specific H3.2 targets including Ephrin family genes. Altered enrichment of H3.2 was found in the mutant Aey69 mouse, specifically around the ligand Efna5 and the receptor Ephb2. The effect of this altered enrichment on Ephrin signaling was further analysed by QPCR and immunohistochemistry. This study identifies Hist2h3c1 encoded H3.2 as an important epigenetic player in ocular development. By binding to specific regions of ocular developmental factors Histone H3.2 facilitates the function of these genes for successful early ocular development.
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Affiliation(s)
- Sharmilee Vetrivel
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany.
| | - Dong-Jiunn Jeffery Truong
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Jochen Graw
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany.
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2
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Dao D, Xie B, Nadeem U, Xiao J, Movahedan A, D’Souza M, Leone V, Hariprasad SM, Chang EB, Sulakhe D, Skondra D. High-Fat Diet Alters the Retinal Transcriptome in the Absence of Gut Microbiota. Cells 2021; 10:cells10082119. [PMID: 34440888 PMCID: PMC8392173 DOI: 10.3390/cells10082119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
The relationship between retinal disease, diet, and the gut microbiome has shown increasing importance over recent years. In particular, high-fat diets (HFDs) are associated with development and progression of several retinal diseases, including age-related macular degeneration (AMD) and diabetic retinopathy. However, the complex, overlapping interactions between diet, gut microbiome, and retinal homeostasis are poorly understood. Using high-throughput RNA-sequencing (RNA-seq) of whole retinas, we compare the retinal transcriptome from germ-free (GF) mice on a regular diet (ND) and HFD to investigate transcriptomic changes without influence of gut microbiome. After correction of raw data, 53 differentially expressed genes (DEGs) were identified, of which 19 were upregulated and 34 were downregulated in GF-HFD mice. Key genes involved in retinal inflammation, angiogenesis, and RPE function were identified. Enrichment analysis revealed that the top 3 biological processes affected were regulation of blood vessel diameter, inflammatory response, and negative regulation of endopeptidase. Molecular functions altered include endopeptidase inhibitor activity, protease binding, and cysteine-type endopeptidase inhibitor activity. Human and mouse pathway analysis revealed that the complement and coagulation cascades are significantly affected by HFD. This study demonstrates novel data that diet can directly modulate the retinal transcriptome independently of the gut microbiome.
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Affiliation(s)
- David Dao
- Department of Ophthalmology and Visual Science, University of Chicago, Chicago, IL 60637, USA; (D.D.); (J.X.); (S.M.H.)
| | - Bingqing Xie
- Center for Research Informatics, University of Chicago, Chicago, IL 60637, USA; (B.X.); (M.D.)
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA;
| | - Urooba Nadeem
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA;
| | - Jason Xiao
- Department of Ophthalmology and Visual Science, University of Chicago, Chicago, IL 60637, USA; (D.D.); (J.X.); (S.M.H.)
| | - Asad Movahedan
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT 06437, USA;
| | - Mark D’Souza
- Center for Research Informatics, University of Chicago, Chicago, IL 60637, USA; (B.X.); (M.D.)
| | - Vanessa Leone
- Department of Animal Biologics and Metabolism, University of Wisconsin, Madison, WI 53706, USA;
- Knapp Center for Biomedical Discovery, Department of Medicine, Microbiome Medicine Program, University of Chicago, Chicago, IL 60637, USA;
| | - Seenu M. Hariprasad
- Department of Ophthalmology and Visual Science, University of Chicago, Chicago, IL 60637, USA; (D.D.); (J.X.); (S.M.H.)
| | - Eugene B. Chang
- Knapp Center for Biomedical Discovery, Department of Medicine, Microbiome Medicine Program, University of Chicago, Chicago, IL 60637, USA;
| | - Dinanath Sulakhe
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA;
| | - Dimitra Skondra
- Department of Ophthalmology and Visual Science, University of Chicago, Chicago, IL 60637, USA; (D.D.); (J.X.); (S.M.H.)
- Correspondence:
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3
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Papadogianni G, Ravens I, Dittrich-Breiholz O, Bernhardt G, Georgiev H. Impact of Aging on the Phenotype of Invariant Natural Killer T Cells in Mouse Thymus. Front Immunol 2020; 11:575764. [PMID: 33193368 PMCID: PMC7662090 DOI: 10.3389/fimmu.2020.575764] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Invariant natural killer T (iNKT) cells represent a subclass of T cells possessing a restricted repertoire of T cell receptors enabling them to recognize lipid derived ligands. iNKT cells are continuously generated in thymus and differentiate into three main subpopulations: iNKT1, iNKT2, and iNKT17 cells. We investigated the transcriptomes of these subsets comparing cells isolated from young adult (6–10 weeks old) and aged BALB/c mice (25–30 weeks of age) in order to identify genes subject to an age-related regulation of expression. These time points were selected to take into consideration the consequences of thymic involution that radically alter the existing micro-milieu. Significant differences were detected in the expression of histone genes affecting all iNKT subsets. Also the proliferative capacity of iNKT cells decreased substantially upon aging. Several genes were identified as possible candidates causing significant age-dependent changes in iNKT cell generation and/or function such as genes coding for granzyme A, ZO-1, EZH2, SOX4, IGF1 receptor, FLT4, and CD25. Moreover, we provide evidence that IL2 differentially affects homeostasis of iNKT subsets with iNKT17 cells engaging a unique mechanism to respond to IL2 by initiating a slow rate of proliferation.
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Affiliation(s)
| | - Inga Ravens
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Günter Bernhardt
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Hristo Georgiev
- Institute of Immunology, Hannover Medical School, Hannover, Germany
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4
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Guan G, He X, Chen J, Bin L, Tang X. Identifying the mechanisms underlying the protective effect of tetramethylpyrazine against cisplatin‑induced in vitro ototoxicity in HEI‑OC1 auditory cells using gene expression profiling. Mol Med Rep 2020; 22:5053-5068. [PMID: 33174043 PMCID: PMC7646960 DOI: 10.3892/mmr.2020.11631] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 06/26/2020] [Indexed: 12/02/2022] Open
Abstract
Sensorineural hearing loss is prevalent in patients receiving cisplatin therapy. Tetramethylpyrazine (Tet) and tanshinone IIA (Tan IIA) have protective roles against hearing impairment or ototoxicity. The present study aimed to investigate the molecular mechanisms underlying cisplatin-induced ototoxicity and the protective effect of Tet and Tan IIA against it. House Ear Institute-Organ of Corti 1 auditory cells were treated with titrating doses of Tan IIA, Tet, and cisplatin. In a cell viability assay, cisplatin, Tan IIA and Tet had IC50 values of 42.89 µM, 151.80 and 1.04×103 mg/l, respectively. Tan IIA augmented cisplatin-induced cytotoxicity. However, Tet concentrations <75 mg/l attenuated cisplatin-induced cytotoxicity and apoptosis. Moreover, RNA sequencing analysis was carried out on auditory cells treated for 30 h with 30 µM cisplatin alone for 48 h or combined with 37.5 mg/l Tet for 30 h. Differentially expressed genes (DEGs) induced in these conditions were identified and examined using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. Cisplatin increased the expression of genes related to the p53 and FoxO pathways, such as Fas, p21/CDKN1A, and Bcl-2 binding component 3, but decreased the expression of insulin-like growth factor 1 (IGF1), as well as genes in the histone (Hist)1 and Hist2 clusters. Treatment with Tet downregulated FOXO3 and Bcl-2 binding component 3, and increased the expression of IGF1. Moreover, Tet upregulated genes associated with Wnt signaling, but not p53-related genes. Thus, the otoprotective properties of Tet might be mediated by activation of Wnt and IGF1 signaling, and inhibition of FoxO signaling.
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Affiliation(s)
- Guofang Guan
- Department of Otolaryngology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Xiao He
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Traditional Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Jingjing Chen
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Traditional Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Li Bin
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Traditional Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Xuxia Tang
- Department of Otolaryngology, The First Affiliated Hospital of Zhejiang Traditional Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
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5
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Abstract
A user-friendly workflow, termed Tomahto, enables real-time targeted pathway proteomics assays using two-dimensional multiplexing technology. Hundreds of proteins of interest from a multitude of samples can be targeted and accurately quantified in a remarkably sensitive fashion. We highlight Tomahto’s ease of use, sensitivity, and accuracy and present proof-of-principle utility by targeting 260 metabolism- and inflammation-related proteins across 90 samples (nine tissues from five old and five young mice). Tissue-specific aging effects are presented with specific interest in metabolic and inflammatory pathways of white adipose tissue. We validated our approach through comparison with a global proteome survey across the tissues, work that we also provide as a general resource for the community. Pathway proteomics strategies measure protein expression changes in specific cellular processes that carry out related functions. Using targeted tandem mass tags-based sample multiplexing, hundreds of proteins can be quantified across 10 or more samples simultaneously. To facilitate these highly complex experiments, we introduce a strategy that provides complete control over targeted sample multiplexing experiments, termed Tomahto, and present its implementation on the Orbitrap Tribrid mass spectrometer platform. Importantly, this software monitors via the external desktop computer to the data stream and inserts optimized MS2 and MS3 scans in real time based on an application programming interface with the mass spectrometer. Hundreds of proteins of interest from diverse biological samples can be targeted and accurately quantified in a sensitive and high-throughput fashion. It achieves sensitivity comparable to, if not better than, deep fractionation and requires minimal total sample input (∼10 µg). As a proof-of-principle experiment, we selected four pathways important in metabolism- and inflammation-related processes (260 proteins/520 peptides) and measured their abundance across 90 samples (nine tissues from five old and five young mice) to explore effects of aging. Tissue-specific aging is presented here and we highlight the role of inflammation- and metabolism-related processes in white adipose tissue. We validated our approach through comparison with a global proteome survey across the tissues, work that we also provide as a general resource for the community.
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6
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Arike L, Seiman A, van der Post S, Rodriguez Piñeiro AM, Ermund A, Schütte A, Bäckhed F, Johansson MEV, Hansson GC. Protein Turnover in Epithelial Cells and Mucus along the Gastrointestinal Tract Is Coordinated by the Spatial Location and Microbiota. Cell Rep 2020; 30:1077-1087.e3. [PMID: 31995731 PMCID: PMC6996021 DOI: 10.1016/j.celrep.2019.12.068] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/09/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from microbial invasion. The epithelium has one of the highest turnover rates in the body. Using stable isotope labeling, high-resolution mass spectrometry, and computational analysis, we report a comprehensive dataset of the turnover of more than 3,000 and the expression of more than 5,000 intestinal epithelial cell proteins, analyzed under conventional and germ-free conditions across five different segments in mouse intestine. The median protein half-life is shorter in the small intestine than in the colon. Differences in protein turnover rates along the intestinal tract can be explained by distinct physiological and immune-related functions between the small and large intestine. An absence of microbiota results in an approximately 1 day longer protein half-life in germ-free animals. Dataset of protein turnover rate and expression along the mice intestinal tract Protein turnover rate is slower in colon than in small intestine Median protein half-life is 1 day longer in germ-free mice
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Affiliation(s)
- Liisa Arike
- Department of Medical Biochemistry, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Andrus Seiman
- Centre of Food and Fermentation Technologies, Akadeemia tee 15a, 12618 Tallinn, Estonia
| | - Sjoerd van der Post
- Department of Medical Biochemistry, University of Gothenburg, 405 30 Gothenburg, Sweden
| | | | - Anna Ermund
- Department of Medical Biochemistry, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - André Schütte
- Department of Medical Biochemistry, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Malin E V Johansson
- Department of Medical Biochemistry, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gunnar C Hansson
- Department of Medical Biochemistry, University of Gothenburg, 405 30 Gothenburg, Sweden.
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7
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MeCP2-E1 isoform is a dynamically expressed, weakly DNA-bound protein with different protein and DNA interactions compared to MeCP2-E2. Epigenetics Chromatin 2019; 12:63. [PMID: 31601272 PMCID: PMC6786283 DOI: 10.1186/s13072-019-0298-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 08/22/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND MeCP2-a chromatin-binding protein associated with Rett syndrome-has two main isoforms, MeCP2-E1 and MeCP2-E2, differing in a few N-terminal amino acid residues. Previous studies have shown brain region-specific expression of these isoforms which, in addition to their different cellular localization and differential expression during brain development, suggest that they may also have non-overlapping molecular mechanisms. However, differential functions of MeCP2-E1 and E2 remain largely unexplored. RESULTS Here, we show that the N-terminal domains (NTD) of MeCP2-E1 and E2 modulate the ability of the methyl-binding domain (MBD) to interact with DNA as well as influencing the turn-over rates, binding dynamics, response to neuronal depolarization, and circadian oscillations of the two isoforms. Our proteomics data indicate that both isoforms exhibit unique interacting protein partners. Moreover, genome-wide analysis using ChIP-seq provide evidence for a shared as well as a specific regulation of different sets of genes. CONCLUSIONS Our study supports the idea that Rett syndrome might arise from simultaneous impairment of cellular processes involving non-overlapping functions of MECP2 isoforms. For instance, MeCP2-E1 mutations might impact stimuli-dependent chromatin regulation, while MeCP2-E2 mutations could result in aberrant ribosomal expression. Overall, our findings provide insight into the functional complexity of MeCP2 by dissecting differential aspects of its two isoforms.
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8
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Overbey EG, da Silveira WA, Stanbouly S, Nishiyama NC, Roque-Torres GD, Pecaut MJ, Zawieja DC, Wang C, Willey JS, Delp MD, Hardiman G, Mao XW. Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina. Sci Rep 2019; 9:13304. [PMID: 31527661 PMCID: PMC6746706 DOI: 10.1038/s41598-019-49453-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/19/2019] [Indexed: 11/08/2022] Open
Abstract
Extended spaceflight has been shown to adversely affect astronaut visual acuity. The purpose of this study was to determine whether spaceflight alters gene expression profiles and induces oxidative damage in the retina. Ten week old adult C57BL/6 male mice were flown aboard the ISS for 35 days and returned to Earth alive. Ground control mice were maintained on Earth under identical environmental conditions. Within 38 (+/-4) hours after splashdown, mice ocular tissues were collected for analysis. RNA sequencing detected 600 differentially expressed genes (DEGs) in murine spaceflight retinas, which were enriched for genes related to visual perception, the phototransduction pathway, and numerous retina and photoreceptor phenotype categories. Twelve DEGs were associated with retinitis pigmentosa, characterized by dystrophy of the photoreceptor layer rods and cones. Differentially expressed transcription factors indicated changes in chromatin structure, offering clues to the observed phenotypic changes. Immunofluorescence assays showed degradation of cone photoreceptors and increased retinal oxidative stress. Total retinal, retinal pigment epithelium, and choroid layer thickness were significantly lower after spaceflight. These results indicate that retinal performance may decrease over extended periods of spaceflight and cause visual impairment.
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Affiliation(s)
- Eliah G Overbey
- University of Washington, Department of Genome Sciences, Seattle, WA, USA.
| | - Willian Abraham da Silveira
- Queen's University Belfast, Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Seta Stanbouly
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Nina C Nishiyama
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
| | | | - Michael J Pecaut
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
| | - David Carl Zawieja
- Department of Medical Physiology, Texas A&M University, College Station, Texas, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Jeffrey S Willey
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Michael D Delp
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Gary Hardiman
- Queen's University Belfast, Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Xiao Wen Mao
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
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9
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Vetrivel S, Tiso N, Kügler A, Irmler M, Horsch M, Beckers J, Hladik D, Giesert F, Gailus-Durner V, Fuchs H, Sabrautzki S, Hrabě de Angelis M, Graw J. Mutation in the mouse histone gene Hist2h3c1 leads to degeneration of the lens vesicle and severe microphthalmia. Exp Eye Res 2019; 188:107632. [PMID: 30991053 PMCID: PMC6876282 DOI: 10.1016/j.exer.2019.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/20/2019] [Accepted: 03/30/2019] [Indexed: 12/21/2022]
Abstract
During an ENU (N-ethyl-N-nitrosourea) mutagenesis screen, we observed a dominant small-eye mutant mouse with viable homozygotes. A corresponding mutant line was established and referred to as Aey69 (abnormality of the eye #69). Comprehensive phenotyping of the homozygous Aey69 mutants in the German Mouse Clinic revealed only a subset of statistically significant alterations between wild types and homozygous mutants. The mutation causes microphthalmia without a lens but with retinal hyperproliferation. Linkage was demonstrated to mouse chromosome 3 between the markers D3Mit188 and D3Mit11. Sequencing revealed a 358 A-> C mutation (Ile120Leu) in the Hist2h3c1 gene and a 71 T-> C (Val24Ala) mutation in the Gja8 gene. Detailed analysis of eye development in the homozygous mutant mice documented a perturbed lens development starting from the lens vesicle stage including decreasing expression of crystallins as well as of lens-specific transcription factors like PITX3 and FOXE3. In contrast, we observed an early expression of retinal progenitor cells characterized by several markers including BRN3 (retinal ganglion cells) and OTX2 (cone photoreceptors). The changes in the retina at the early embryonic stages of E11.5-E15.5 happen in parallel with apoptotic processes in the lens at the respective stages. The excessive retinal hyperproliferation is characterized by an increased level of Ki67. The hyperproliferation, however, does not disrupt the differentiation and appearance of the principal retinal cell types at postnatal stages, even if the overgrowing retina covers finally the entire bulbus of the eye. Morpholino-mediated knock-down of the hist2h3ca1 gene in zebrafish leads to a specific perturbation of lens development. When injected into zebrafish zygotes, only the mutant mouse mRNA leads to severe malformations, ranging from cyclopia to severe microphthalmia. The wild-type Hist2h3c1 mRNA can rescue the morpholino-induced defects corroborating its specific function in lens development. Based upon these data, it is concluded that the ocular function of the Hist2h3c1 gene (encoding a canonical H3.2 variant) is conserved throughout evolution. Moreover, the data highlight also the importance of Hist2h3c1 in the coordinated formation of lens and retina during eye development. A dominant small-eye mutant mouse is caused by a mutation in the histone gene Hist2H3c1. Morpholino-mediated knock-down of hist2h3ca1 in the zebrafish validated this finding. The mutation leads to degeneration of the lens vesicle and retina hyperproliferation.
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Affiliation(s)
- Sharmilee Vetrivel
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Natascia Tiso
- Department of Biology, University of Padova, I-35131 Padova, Italy.
| | - Andrea Kügler
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Martin Irmler
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Marion Horsch
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Johannes Beckers
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, D-85354 Freising, Germany; German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
| | - Daniela Hladik
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Florian Giesert
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Helmut Fuchs
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany
| | - Sibylle Sabrautzki
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Comparative Medicine, D-85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Experimental Genetics, D-85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, D-85354 Freising, Germany; German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
| | - Jochen Graw
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany.
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Baumgartner M, Olthof AM, Aquino GS, Hyatt KC, Lemoine C, Drake K, Sturrock N, Nguyen N, Al Seesi S, Kanadia RN. Minor spliceosome inactivation causes microcephaly, owing to cell cycle defects and death of self-amplifying radial glial cells. Development 2018; 145:dev.166322. [PMID: 30093551 DOI: 10.1242/dev.166322] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/13/2018] [Indexed: 12/13/2022]
Abstract
Mutation in minor spliceosome components is linked to the developmental disorder microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). Here, we inactivated the minor spliceosome in the developing mouse cortex (pallium) by ablating Rnu11, which encodes the crucial minor spliceosome small nuclear RNA (snRNA) U11. Rnu11 conditional knockout mice were born with microcephaly, which was caused by the death of self-amplifying radial glial cells (RGCs), while intermediate progenitor cells and neurons were produced. RNA sequencing suggested that this cell death was mediated by upregulation of p53 (Trp53 - Mouse Genome Informatics) and DNA damage, which were both observed specifically in U11-null RGCs. Moreover, U11 loss caused elevated minor intron retention in genes regulating the cell cycle, which was consistent with fewer RGCs in S-phase and cytokinesis, alongside prolonged metaphase in RGCs. In all, we found that self-amplifying RGCs are the cell type most sensitive to loss of minor splicing. Together, these findings provide a potential explanation of how disruption of minor splicing might cause microcephaly in MOPD1.
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Affiliation(s)
- Marybeth Baumgartner
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabriela S Aquino
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Katery C Hyatt
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Christopher Lemoine
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,College of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Kyle Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Nikita Sturrock
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Nhut Nguyen
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Sahar Al Seesi
- Computer Science Engineering Department, University of Connecticut, Storrs, CT 06269, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA .,Institute of Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro. Skelet Muscle 2017; 7:5. [PMID: 28381300 PMCID: PMC5382473 DOI: 10.1186/s13395-017-0122-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/16/2017] [Indexed: 12/21/2022] Open
Abstract
Background The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. As such, the spatial organization of a genome represents a window on the genome biology that enables analysis of the nuclear regulatory processes that contribute to mammalian development. Methods In this study, Hi-C and RNA-seq were used to capture the genome organization and transcriptome in mouse muscle progenitor cells (C2C12 myoblasts) before and after differentiation to myotubes, in the presence or absence of the cytidine analogue AraC. Results We observed significant local and global developmental changes despite high levels of correlation between the myotubes and myoblast genomes. Notably, the genes that exhibited the greatest variation in transcript levels between the different developmental stages were predominately within the euchromatic compartment. There was significant re-structuring and changes in the expression of replication-dependent histone variants within the HIST1 locus. Finally, treating terminally differentiated myotubes with AraC resulted in additional changes to the transcriptome and 3D genome organization of sets of genes that were all involved in pyroptosis. Conclusions Collectively, our results provide evidence for muscle cell-specific responses to developmental and environmental stimuli mediated through a chromatin structure mechanism. Electronic supplementary material The online version of this article (doi:10.1186/s13395-017-0122-1) contains supplementary material, which is available to authorized users.
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Karunakaran DKP, Al Seesi S, Banday AR, Baumgartner M, Olthof A, Lemoine C, Măndoiu II, Kanadia RN. Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development. BMC Genomics 2016; 17 Suppl 5:495. [PMID: 27586787 PMCID: PMC5009874 DOI: 10.1186/s12864-016-2822-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The retina as a model system with extensive information on genes involved in development/maintenance is of great value for investigations employing deep sequencing to capture transcriptome change over time. This in turn could enable us to find patterns in gene expression across time to reveal transition in biological processes. Methods We developed a bioinformatics pipeline to categorize genes based on their differential expression and their alternative splicing status across time by binning genes based on their transcriptional kinetics. Genes within same bins were then leveraged to query gene annotation databases to discover molecular programs employed by the developing retina. Results Using our pipeline on RNA-Seq data obtained from fractionated (nucleus/cytoplasm) developing retina at embryonic day (E) 16 and postnatal day (P) 0, we captured high-resolution as in the difference between the cytoplasm and the nucleus at the same developmental time. We found de novo transcription of genes whose transcripts were exclusively found in the nuclear transcriptome at P0. Further analysis showed that these genes enriched for functions that are known to be executed during postnatal development, thus showing that the P0 nuclear transcriptome is temporally ahead of that of its cytoplasm. We extended our strategy to perform temporal analysis comparing P0 data to either P21-Nrl-wildtype (WT) or P21-Nrl-knockout (KO) retinae, which predicted that the KO retina would have compromised vasculature. Indeed, histological manifestation of vasodilation has been reported at a later time point (P60). Conclusions Thus, our approach was predictive of a phenotype before it presented histologically. Our strategy can be extended to investigating the development and/or disease progression of other tissue types. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2822-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sahar Al Seesi
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Abdul Rouf Banday
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269, USA
| | - Marybeth Baumgartner
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269, USA
| | - Anouk Olthof
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269, USA.,Utrecht University, 3508 TC, Utrecht, The Netherlands
| | - Christopher Lemoine
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269, USA
| | - Ion I Măndoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Rahul N Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269, USA.
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Henning Y, Szafranski K. Age-Dependent Changes of Monocarboxylate Transporter 8 Availability in the Postnatal Murine Retina. Front Cell Neurosci 2016; 10:205. [PMID: 27616981 PMCID: PMC4999454 DOI: 10.3389/fncel.2016.00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/15/2016] [Indexed: 12/12/2022] Open
Abstract
The thyroid hormones (TH) triiodothyronine (T3) and its prohormone thyroxine (T4) are crucial for retinal development and function, and increasing evidence points at TH dysregulation as a cause for retinal degenerative diseases. Thus, precise regulation of retinal TH supply is required for proper retinal function, but knowledge on these mechanisms is still fragmentary. Several transmembrane transporters have been described as key regulators of TH availability in target tissues of which the monocarboxylate transporter 8 (MCT8), a high affinity transporter for T4 and T3, plays an essential role in the central nervous system. Moreover, in the embryonic chicken retina, MCT8 is highly expressed, but the postnatal availability of MCT8 in the mammalian retina was not reported to date. In the present study, spatiotemporal retinal MCT8 availability was examined in mice of different age. For this purpose, we quantified expression levels of Mct8 via Real-Time Reverse-Transcriptase PCR in mouse eyecups (C57BL/6) of juvenile and adult age groups. Additionally, age-dependent MCT8 protein levels were quantified via Western blotting and localized via immunofluorescence confocal microscopy. While no difference in Mct8 expression levels could be detected between age groups, MCT8 protein levels in juvenile animals were about two times higher than in adult animals based on Western blot analyses. Immunohistochemical analyses showed that MCT8 immunoreactivity in the eyecup was restricted to the retina and the retinal pigment epithelium. In juvenile mice, MCT8 was broadly observed along the apical membrane of the retinal pigment epithelium, tightly surrounding photoreceptor outer segments. Distinct immunopositive staining was also detected in the inner nuclear layer and the ganglion cell layer. However, in adult specimens, immunoreactivity visibly declined in all layers, which was in line with Western blot analyses. Since MCT8 was abundantly present in juvenile and about twofold lower in adult retinae, our findings suggest a pivotal role of MCT8 especially during postnatal maturation. The present study provides novel insights into age-dependent retinal TH supply, which might help to understand different aspects regarding retinal development, function, and disorders.
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Affiliation(s)
- Yoshiyuki Henning
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen Essen, Germany
| | - Karol Szafranski
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute Jena, Germany
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Ausió J. MeCP2 and the enigmatic organization of brain chromatin. Implications for depression and cocaine addiction. Clin Epigenetics 2016; 8:58. [PMID: 27213019 PMCID: PMC4875624 DOI: 10.1186/s13148-016-0214-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022] Open
Abstract
Methyl CpG binding protein 2 (MeCP2) is a highly abundant chromosomal protein within the brain. It is hence not surprising that perturbations in its genome-wide distribution, and at particular loci within this tissue, can result in widespread neurological disorders that transcend the early implications of this protein in Rett syndrome (RTT). Yet, the details of its role and involvement in chromatin organization are still poorly understood. This paper focuses on what is known to date about all of this with special emphasis on the relation to different epigenetic modifications (DNA methylation, histone acetylation/ubiquitination, MeCP2 phosphorylation and miRNA). We showcase all of the above in two particular important neurological functional alterations in the brain: depression (major depressive disorder [MDD]) and cocaine addiction, both of which affect the MeCP2 homeostasis and result in significant changes in the overall levels of these epigenetic marks.
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Affiliation(s)
- Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6 Canada
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Noce A, Canale MP, Capria A, Rovella V, Tesauro M, Splendiani G, Annicchiarico-Petruzzelli M, Manzuoli M, Simonetti G, Di Daniele N. Coronary artery calcifications predict long term cardiovascular events in non diabetic Caucasian hemodialysis patients. Aging (Albany NY) 2016; 7:269-79. [PMID: 26131456 PMCID: PMC4429091 DOI: 10.18632/aging.100740] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Vascular calcifications are frequent in chronic renal disease and are associated to significant cardiovascular morbidity and mortality. The long term predictive value of coronary artery calcifications detected by multi-layer spiral computed tomography for major cardiovascular events was evaluated in non-diabetic Caucasian patients on maintenance hemodialysis free of clinical cardiovascular disease. Two-hundred and five patients on maintenance hemodialysis were enrolled into this observational, prospective cohort study. Patients underwent a single cardiac multi-layer spiral computed tomography. Calcium load was quantified and patients grouped according to the Agatston score: group 1 (Agatston score: 0), group 2 (Agatston score 1-400), group 3 (Agatston score 401-1000) and group 4 (Agatston score >1000). Follow-up was longer than seven years. Primary endpoint was death from a major cardiovascular event. Actuarial survival was calculated separately in the four groups with Kaplan-Meier method. Patients who died from causes other than cardiovascular disease and transplanted patients were censored. The “log rank” test was employed to compare survival curves. One-hundred two patients (49.7%) died for a major cardiovascular event during the follow-up period. Seven-year actuarial survival was more than 90% for groups 1 and 2, but failed to about 50% for group 3 and to <10% for group 4. Hence, Agatston score >400 predicts a significantly higher cardiovascular mortality compared with Agatston score <400 (p<0.0001); furthermore, serum Parathyroid hormone levels > 300 pg/l were associated to a lower survival (p < 0.05). Extended coronary artery calcifications detected by cardiac multi-layer spiral computed tomography, strongly predicted long term cardiovascular mortality in non-diabetic Caucasian patients on maintenance hemodialysis. Moreover, it was not related to conventional indices of atherosclerosis, but to other non-traditional risk factors, as serum Parathyroid hormone levels. A full cost-benefit analysis is however necessary to justify a widespread use of cardiac multi-layer spiral computed tomography in clinical practice.
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Baumgartner M, Lemoine C, Al Seesi S, Karunakaran DKP, Sturrock N, Banday AR, Kilcollins AM, Mandoiu I, Kanadia RN. Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons. Dev Neurobiol 2014; 75:895-907. [PMID: 25492806 DOI: 10.1002/dneu.22257] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/24/2014] [Accepted: 12/08/2014] [Indexed: 12/21/2022]
Abstract
In eukaryotes, gene expression requires splicing, which starts with the identification of exon-intron boundaries by the small, nuclear RNA (snRNAs) of the spliceosome, aided by associated proteins. In the mammalian genome, <1% of introns lack canonical exon-intron boundary sequences and cannot be spliced by the canonical splicing machinery. These introns are spliced by the minor spliceosome, consisting of unique snRNAs (U11, U12, U4atac, and U6atac). The importance of the minor spliceosome is underscored by the disease microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1), which is caused by mutation in U4atac. Thus, it is important to understand the expression and function of the minor spliceosome and its targets in mammalian development, for which we used the mouse as our model. Here, we report enrichment of the minor snRNAs in the developing head/central nervous system (CNS) between E9.5 and E12.5, along with enrichment of these snRNAs in differentiating retinal neurons. Moreover, dynamic expression kinetics of minor intron-containing genes (MIGs) was observed across retinal development. DAVID analysis of MIGs that were cotranscriptionally upregulated embryonically revealed enrichment for RNA metabolism and cell cycle regulation. In contrast, MIGs that were cotranscriptionally upregulated postnatally revealed enrichment for protein localization/transport, vesicle-mediated transport, and calcium transport. Finally, we used U12 morpholino to inactivate the minor spliceosome in the postnatal retina, which resulted in apoptosis of differentiating retinal neurons. Taken together, our data suggest that the minor spliceosome may have distinct functions in embryonic versus postnatal development. Importantly, we show that the minor spliceosome is crucial for the survival of terminally differentiating retinal neurons.
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Affiliation(s)
- Marybeth Baumgartner
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Christopher Lemoine
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Sahar Al Seesi
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, 06269
| | | | - Nikita Sturrock
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Abdul Rouf Banday
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Ashley M Kilcollins
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Ion Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, 06269
| | - Rahul N Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
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