1
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von Berlin L, Westholm JO, Ratz M, Frisén J. Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis. Hippocampus 2023; 33:391-401. [PMID: 36468233 DOI: 10.1002/hipo.23482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/17/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022]
Abstract
Hippocampal adult neural stem cells emerge from progeny of the neuroepithelial lineage during murine brain development. Hippocampus development is increasingly well understood. However, the clonal relationships between early neuroepithelial stem cells and postnatal neurogenic cells remain unclear, especially at the single-cell level. Here we report fate bias and gene expression programs in thousands of clonally related cells in the juvenile hippocampus based on single-cell RNA-seq of barcoded clones. We find evidence for early fate restriction of neuroepithelial stem cells to either neurogenic progenitor cells of the dentate gyrus region or oligodendrogenic, non-neurogenic fate supplying cells for other hippocampal regions including gray matter areas and the Cornu ammonis region 1/3. Our study provides new insights into the phenomenon of early fate restriction guiding the development of postnatal hippocampal neurogenesis.
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Affiliation(s)
- Leonie von Berlin
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- KTH Royal Institute of Technology, Department of Gene Technology, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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2
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Mateus Brandão LE, Espes D, Westholm JO, Martikainen T, Westerlund N, Lampola L, Popa A, Vogel H, Schürmann A, Dickson SL, Benedict C, Cedernaes J. Acute sleep loss alters circulating fibroblast growth factor 21 levels in humans: A randomised crossover trial. J Sleep Res 2021; 31:e13472. [PMID: 34476847 DOI: 10.1111/jsr.13472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/14/2021] [Accepted: 08/12/2021] [Indexed: 12/11/2022]
Abstract
The hormone fibroblast growth factor 21 (FGF21) modulates tissue metabolism and circulates at higher levels in metabolic conditions associated with chronic sleep-wake disruption, such as type 2 diabetes and obesity. In the present study, we investigated whether acute sleep loss impacts circulating levels of FGF21 and tissue-specific production, and response pathways linked to FGF21. A total of 15 healthy normal-weight young men participated in a randomised crossover study with two conditions, sleep loss versus an 8.5-hr sleep window. The evening before each intervention, fasting blood was collected. Fasting, post-intervention morning skeletal muscle and adipose tissue samples underwent quantitative polymerase chain reaction and DNA methylation analyses, and serum FGF21 levels were measured before and after an oral glucose tolerance test. Serum levels of FGF21 were higher after sleep loss compared with sleep, both under fasting conditions and following glucose intake (~27%-30%, p = 0.023). Fasting circulating levels of fibroblast activation protein, a protein which can degrade circulating FGF21, were not altered by sleep loss, whereas DNA methylation in the FGF21 promoter region increased only in adipose tissue. However, even though specifically the muscle exhibited transcriptional changes indicating adverse alterations to redox and metabolic homeostasis, no tissue-based changes were observed in expression of FGF21, its receptors, or selected signalling targets, in response to sleep loss. In summary, we found that acute sleep loss resulted in increased circulating levels of FGF21 in healthy young men, which may occur independent of a tissue-based stress response in metabolic peripheral tissues. Further studies may decipher whether changes in FGF21 signalling after sleep loss modulate metabolic outcomes associated with sleep or circadian disruption.
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Affiliation(s)
| | - Daniel Espes
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | | | - Lauri Lampola
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Alexandru Popa
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Heike Vogel
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany.,German Center for Diabetes Research, Neuherberg, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, , The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany.,German Center for Diabetes Research, Neuherberg, Germany
| | - Suzanne L Dickson
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | | | - Jonathan Cedernaes
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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3
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Sork H, Conceicao M, Corso G, Nordin J, Lee YXF, Krjutskov K, Orzechowski Westholm J, Vader P, Pauwels M, Vandenbroucke RE, Wood MJA, EL Andaloussi S, Mäger I. Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion. Cells 2021; 10:1543. [PMID: 34207405 PMCID: PMC8235078 DOI: 10.3390/cells10061543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
The extracellular environment consists of a plethora of molecules, including extracellular miRNA that can be secreted in association with extracellular vesicles (EVs) or soluble protein complexes (non-EVs). Yet, interest in therapeutic short RNA carriers lies mainly in EVs, the vehicles conveying the great majority of the biological activity. Here, by overexpressing miRNA and shRNA sequences in parent cells and using size exclusion liquid chromatography (SEC) to separate the secretome into EV and non-EV fractions, we saw that >98% of overexpressed miRNA was secreted within the non-EV fraction. Furthermore, small RNA sequencing studies of native miRNA transcripts revealed that although the abundance of miRNAs in EVs, non-EVs and parent cells correlated well (R2 = 0.69-0.87), quantitatively an outstanding 96.2-99.9% of total miRNA was secreted in the non-EV fraction. Nevertheless, though EVs contained only a fraction of secreted miRNAs, these molecules were stable at 37 °C in a serum-containing environment, indicating that if sufficient miRNA loading is achieved, EVs can remain delivery-competent for a prolonged period of time. This study suggests that the passive endogenous EV loading strategy might be a relatively wasteful way of loading miRNA to EVs, and active miRNA loading approaches are needed for developing advanced EV miRNA therapies in the future.
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Affiliation(s)
- Helena Sork
- Department of Laboratory Medicine, Karolinska Institutet, SE-141 52 Huddinge, Sweden; (G.C.); (J.N.); (S.E.A.)
- Institute of Technology, University of Tartu, 50 411 Tartu, Estonia
| | - Mariana Conceicao
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK; (M.C.); (Y.X.F.L.); (M.J.W.)
| | - Giulia Corso
- Department of Laboratory Medicine, Karolinska Institutet, SE-141 52 Huddinge, Sweden; (G.C.); (J.N.); (S.E.A.)
| | - Joel Nordin
- Department of Laboratory Medicine, Karolinska Institutet, SE-141 52 Huddinge, Sweden; (G.C.); (J.N.); (S.E.A.)
- Evox Therapeutics, King Charles House, Oxford OX1 1JD, UK
| | - Yi Xin Fiona Lee
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK; (M.C.); (Y.X.F.L.); (M.J.W.)
| | - Kaarel Krjutskov
- Competence Centre on Health Technologies, 50 411 Tartu, Estonia;
| | - Jakub Orzechowski Westholm
- Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna, Box 1031, SE-171 21 Stockholm, Sweden;
| | - Pieter Vader
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
- Department of Experimental Cardiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Marie Pauwels
- Barriers in Inflammation Lab, VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium; (M.P.); (R.E.V.)
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Roosmarijn E. Vandenbroucke
- Barriers in Inflammation Lab, VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium; (M.P.); (R.E.V.)
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Matthew JA Wood
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK; (M.C.); (Y.X.F.L.); (M.J.W.)
- MDUK Oxford Neuromuscular Centre, Oxford OX1 3QX, UK
| | - Samir EL Andaloussi
- Department of Laboratory Medicine, Karolinska Institutet, SE-141 52 Huddinge, Sweden; (G.C.); (J.N.); (S.E.A.)
| | - Imre Mäger
- Institute of Technology, University of Tartu, 50 411 Tartu, Estonia
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK; (M.C.); (Y.X.F.L.); (M.J.W.)
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4
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Zaghlool A, Niazi A, Björklund ÅK, Westholm JO, Ameur A, Feuk L. Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts. Sci Rep 2021; 11:4076. [PMID: 33603054 PMCID: PMC7893067 DOI: 10.1038/s41598-021-83541-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 01/20/2021] [Indexed: 12/23/2022] Open
Abstract
Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.
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Affiliation(s)
- Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden. .,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden.
| | - Adnan Niazi
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden.,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden
| | - Åsa K Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden.,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Uppsala University, BMC B11:4, Box 815, 751 08, Uppsala, Sweden. .,Science for Life Laboratory in Uppsala, Uppsala University, Uppsala, Sweden.
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5
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Zaghlool A, Ameur A, Wu C, Westholm JO, Niazi A, Manivannan M, Bramlett K, Nilsson M, Feuk L. Expression profiling and in situ screening of circular RNAs in human tissues. Sci Rep 2018; 8:16953. [PMID: 30446675 PMCID: PMC6240052 DOI: 10.1038/s41598-018-35001-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/28/2018] [Indexed: 12/23/2022] Open
Abstract
Circular RNAs (circRNAs) were recently discovered as a class of widely expressed noncoding RNA and have been implicated in regulation of gene expression. However, the function of the majority of circRNAs remains unknown. Studies of circRNAs have been hampered by a lack of essential approaches for detection, quantification and visualization. We therefore developed a target-enrichment sequencing method suitable for screening of circRNAs and their linear counterparts in large number of samples. We also applied padlock probes and in situ sequencing to visualize and determine circRNA localization in human brain tissue at subcellular levels. We measured circRNA abundance across different human samples and tissues. Our results highlight the potential of this RNA class to act as a specific diagnostic marker in blood and serum, by detection of circRNAs from genes exclusively expressed in the brain. The powerful and scalable tools we present will enable studies of circRNA function and facilitate screening of circRNA as diagnostic biomarkers.
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Affiliation(s)
- Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Chenglin Wu
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jakub Orzechowski Westholm
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Adnan Niazi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Manimozhi Manivannan
- Clinical Sequencing Division, Life Science Solutions Group, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Kelli Bramlett
- Clinical Sequencing Division, Life Science Solutions Group, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Mats Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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6
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Cedernaes J, Schönke M, Westholm JO, Mi J, Chibalin A, Voisin S, Osler M, Vogel H, Hörnaeus K, Dickson SL, Lind SB, Bergquist J, Schiöth HB, Zierath JR, Benedict C. Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans. Sci Adv 2018; 4:eaar8590. [PMID: 30140739 PMCID: PMC6105229 DOI: 10.1126/sciadv.aar8590] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Curtailed sleep promotes weight gain and loss of lean mass in humans, although the underlying molecular mechanisms are poorly understood. We investigated the genomic and physiological impact of acute sleep loss in peripheral tissues by obtaining adipose tissue and skeletal muscle after one night of sleep loss and after one full night of sleep. We find that acute sleep loss alters genome-wide DNA methylation in adipose tissue, and unbiased transcriptome-, protein-, and metabolite-level analyses also reveal highly tissue-specific changes that are partially reflected by altered metabolite levels in blood. We observe transcriptomic signatures of inflammation in both tissues following acute sleep loss, but changes involving the circadian clock are evident only in skeletal muscle, and we uncover molecular signatures suggestive of muscle breakdown that contrast with an anabolic adipose tissue signature. Our findings provide insight into how disruption of sleep and circadian rhythms may promote weight gain and sarcopenia.
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Affiliation(s)
| | - Milena Schönke
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Sweden
| | - Jakub Orzechowski Westholm
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jia Mi
- Department of Chemistry–BMC, Uppsala University, Uppsala, Sweden
- Medicine and Pharmarcy Research Center, Binzhou Medical University, Yantai, China
| | - Alexander Chibalin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Sweden
| | - Sarah Voisin
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Megan Osler
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Sweden
| | - Heike Vogel
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Potsdam, Germany
| | | | - Suzanne L. Dickson
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Jonas Bergquist
- Department of Chemistry–BMC, Uppsala University, Uppsala, Sweden
- Department of Pathology, University of Utah, Salt Lake City, UT 84132, USA
- Precision Medicine, Binzhou Medical University, Yantai, China
| | - Helgi B Schiöth
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Juleen R. Zierath
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Sweden
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7
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Orzechowski Westholm J, Tronnersjö S, Nordberg N, Olsson I, Komorowski J, Ronne H. Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cells. PLoS One 2012; 7:e31577. [PMID: 22363679 PMCID: PMC3283669 DOI: 10.1371/journal.pone.0031577] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 01/09/2012] [Indexed: 01/10/2023] Open
Abstract
Aging in organisms as diverse as yeast, nematodes, and mammals is delayed by caloric restriction, an effect mediated by the nutrient sensing TOR, RAS/cAMP, and AKT/Sch9 pathways. The transcription factor Gis1 functions downstream of these pathways in extending the lifespan of nutrient restricted yeast cells, but the mechanisms involved are still poorly understood. We have used gene expression microarrays to study the targets of Gis1 and the related protein Rph1 in different growth phases. Our results show that Gis1 and Rph1 act both as repressors and activators, on overlapping sets of genes as well as on distinct targets. Interestingly, both the activities and the target specificities of Gis1 and Rph1 depend on the growth phase. Thus, both proteins are associated with repression during exponential growth, targeting genes with STRE or PDS motifs in their promoters. After the diauxic shift, both become involved in activation, with Gis1 acting primarily on genes with PDS motifs, and Rph1 on genes with STRE motifs. Significantly, Gis1 and Rph1 control a number of genes involved in acetate and glycerol formation, metabolites that have been implicated in aging. Furthermore, several genes involved in acetyl-CoA metabolism are downregulated by Gis1.
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Affiliation(s)
- Jakub Orzechowski Westholm
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
| | - Susanna Tronnersjö
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Niklas Nordberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ida Olsson
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Komorowski
- Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hans Ronne
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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8
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Sun K, Westholm JO, Tsurudome K, Hagen JW, Lu Y, Kohwi M, Betel D, Gao FB, Haghighi AP, Doe CQ, Lai EC. Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutants. PLoS Genet 2012; 8:e1002515. [PMID: 22347817 PMCID: PMC3276548 DOI: 10.1371/journal.pgen.1002515] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 12/15/2011] [Indexed: 01/31/2023] Open
Abstract
miR-124 is conserved in sequence and neuronal expression across the animal kingdom and is predicted to have hundreds of mRNA targets. Diverse defects in neural development and function were reported from miR-124 antisense studies in vertebrates, but a nematode knockout of mir-124 surprisingly lacked detectable phenotypes. To provide genetic insight from Drosophila, we deleted its single mir-124 locus and found that it is dispensable for gross aspects of neural specification and differentiation. On the other hand, we detected a variety of mutant phenotypes that were rescuable by a mir-124 genomic transgene, including short lifespan, increased dendrite variation, impaired larval locomotion, and aberrant synaptic release at the NMJ. These phenotypes reflect extensive requirements of miR-124 even under optimal culture conditions. Comparison of the transcriptomes of cells from wild-type and mir-124 mutant animals, purified on the basis of mir-124 promoter activity, revealed broad upregulation of direct miR-124 targets. However, in contrast to the proposed mutual exclusion model for miR-124 function, its functional targets were relatively highly expressed in miR-124–expressing cells and were not enriched in genes annotated with epidermal expression. A notable aspect of the direct miR-124 network was coordinate targeting of five positive components in the retrograde BMP signaling pathway, whose activation in neurons increases synaptic release at the NMJ, similar to mir-124 mutants. Derepression of the direct miR-124 target network also had many secondary effects, including over-activity of other post-transcriptional repressors and a net incomplete transition from a neuroblast to a neuronal gene expression signature. Altogether, these studies demonstrate complex consequences of miR-124 loss on neural gene expression and neurophysiology. microRNAs are abundant ∼22 nucleotide RNAs inferred to mediate pervasive post-transcriptional control of most genes. Still, relatively little is understood about their endogenous requirements and impact, especially in animal systems. We analyzed a knockout of Drosophila mir-124, which is conserved in sequence and neuronal expression across the animal kingdom, and predicted to have hundreds of mRNA targets. While dispensable for gross neural specification and differentiation, deletion of mir-124 caused short lifespan, increased variation in dendrite numbers, impaired larval locomotion, and aberrant synaptic release at the NMJ. These phenotypes reflect extensive requirements of miR-124 even under optimal culture conditions. Loss of miR-124 broadly upregulated its direct targets but did not support the proposed mutual exclusion model, as its functional target genes were relatively highly expressed in neurons. One notable aspect of the direct miR-124 network was coordinate targeting of five positive components in the retrograde BMP signaling pathway, whose activation in neurons phenocopies loss of miR-124. Derepression of the direct miR-124 target network had many secondary effects, including over-activity of other post-transcriptional repressors and impaired transition from neuroblast to neuronal transcriptome signatures. Altogether, we demonstrate complex requirements for this conserved miRNA on gene expression and neurophysiology.
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Affiliation(s)
- Kailiang Sun
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, USA
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9
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Zhu X, Zhang Y, Bjornsdottir G, Liu Z, Quan A, Costanzo M, Dávila López M, Westholm JO, Ronne H, Boone C, Gustafsson CM, Myers LC. Histone modifications influence mediator interactions with chromatin. Nucleic Acids Res 2011; 39:8342-54. [PMID: 21742760 PMCID: PMC3201872 DOI: 10.1093/nar/gkr551] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator-histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.
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Affiliation(s)
- Xuefeng Zhu
- Department of Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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10
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Kristell C, Orzechowski Westholm J, Olsson I, Ronne H, Komorowski J, Bjerling P. Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes. Genome Res 2010; 20:361-71. [PMID: 20086243 DOI: 10.1101/gr.098558.109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady-state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promoter regions but only minor effects in coding regions. Here, we describe the short-term response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. Nitrogen depletion leads to a fast induction of a large number of genes in S. pombe and is thus suitable for genome-wide studies of chromatin dynamics during gene regulation. After 20 min of nitrogen removal, 118 transcripts were up-regulated. The distribution of regulated genes throughout the genome was not random; many up-regulated genes were found in clusters, while large parts of the genome were devoid of up-regulated genes. Surprisingly, this up-regulation was associated with nucleosome eviction of equal magnitudes in the promoters and in the coding regions. The nucleosome loss was not limited to induction by nitrogen depletion but also occurred during cadmium treatment. Furthermore, the lower nucleosome density persisted for at least 60 min after induction. Two highly induced genes, urg1(+) and urg2(+), displayed a substantial nucleosome loss, with only 20% of the nucleosomes being left in the coding region. We conclude that nucleosome loss during transcriptional activation is not necessarily limited to promoter regions.
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Affiliation(s)
- Carolina Kristell
- Department of Medical Biochemistry and Microbiology (IMBIM), University of Uppsala, SE-751 23 Uppsala, Sweden
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Mellberg S, Dimberg A, Bahram F, Hayashi M, Rennel E, Ameur A, Westholm JO, Larsson E, Lindahl P, Cross MJ, Claesson-Welsh L. Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis. FASEB J 2009; 23:1490-502. [PMID: 19136612 DOI: 10.1096/fj.08-123810] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To define molecular events accompanying formation of the 3-dimensional (3D) vascular tube, we have characterized gene expression during vascular endothelial growth factor (VEGF)-induced tubular morphogenesis of endothelial cells. Microarray analyses were performed comparing gene induction in growth-arrested, tube-forming endothelial cells harvested from 3D collagen cultures to that in proliferating endothelial cells cultured on fibronectin. Differentially expressed genes were clustered and analyzed for specific endothelial expression through publicly available datasets. We validated the contribution of one of the identified genes, vascular endothelial protein tyrosine phosphatase (VE-PTP), to endothelial morphogenesis. Silencing of VE-PTP expression was accompanied by increased VEGF receptor-2 (VEGFR2) tyrosine phosphorylation and activation of downstream signaling pathways. The increased VEGFR2 activity promoted endothelial cell cycle progression, overcoming the G(0)/G(1) arrest associated with organization into tubular structures in the 3D cultures. Proximity ligation showed close association between VEGFR2 and VE-PTP in resting cells. Activation of VEGFR2 by VEGF led to rapid loss of association, which was resumed with time in parallel with decreased receptor activity. In conclusion, we have identified genes, which may serve critical functions in formation of the vascular tube. One of these, VE-PTP, regulates VEGFR2 activity thereby modulating the VEGF-response during angiogenesis.
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Affiliation(s)
- Sofie Mellberg
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, S-751 85 Uppsala, Sweden
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Westholm JO, Nordberg N, Murén E, Ameur A, Komorowski J, Ronne H. Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3. BMC Genomics 2008; 9:601. [PMID: 19087243 PMCID: PMC2631581 DOI: 10.1186/1471-2164-9-601] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 12/16/2008] [Indexed: 01/06/2023] Open
Abstract
Background Expression of a large number of yeast genes is repressed by glucose. The zinc finger protein Mig1 is the main effector in glucose repression, but yeast also has two related proteins: Mig2 and Mig3. We have used microarrays to study global gene expression in all possible combinations of mig1, mig2 and mig3 deletion mutants. Results Mig1 and Mig2 repress a largely overlapping set of genes on 2% glucose. Genes that are upregulated in a mig1 mig2 double mutant were grouped according to the contribution of Mig2. Most of them show partially redundant repression, with Mig1 being the major repressor, but some genes show complete redundancy, and some are repressed only by Mig1. Several redundantly repressed genes are involved in phosphate metabolism. The promoters of these genes are enriched for Pho4 sites, a novel GGGAGG motif, and a variant Mig1 site which is absent from genes repressed only by Mig1. Genes repressed only by Mig1 on 2% glucose include the hexose transporter gene HXT4, but Mig2 contributes to HXT4 repression on 10% glucose. HXT6 is one of the few genes that are more strongly repressed by Mig2. Mig3 does not seem to overlap in function with Mig1 and Mig2. Instead, Mig3 downregulates the SIR2 gene encoding a histone deacetylase involved in gene silencing and the control of aging. Conclusion Mig2 fine-tunes glucose repression by targeting a subset of the Mig1-repressed genes, and by responding to higher glucose concentrations. Mig3 does not target the same genes as Mig1 and Mig2, but instead downregulates the SIR2 gene.
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Westholm JO, Xu F, Ronne H, Komorowski J. Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation. BMC Bioinformatics 2008; 9:484. [PMID: 19014636 PMCID: PMC2629780 DOI: 10.1186/1471-2105-9-484] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 11/17/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation. RESULTS In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. CONCLUSION We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.
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Rennel E, Mellberg S, Dimberg A, Petersson L, Botling J, Ameur A, Westholm JO, Komorowski J, Lassalle P, Cross MJ, Gerwins P. Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer. Exp Cell Res 2007; 313:1285-94. [PMID: 17362927 DOI: 10.1016/j.yexcr.2007.01.021] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2006] [Revised: 01/06/2007] [Accepted: 01/10/2007] [Indexed: 12/16/2022]
Abstract
An in vitro model of VEGF-A-induced angiogenesis was used to generate transcription profiles of human microvascular endothelial cells. Microarray analysis showed increased transcription of genes known to regulate angiogenesis, but also genes that previously have not been firmly associated with angiogenesis such as endocan, pinin, plakophilin, phosphodiesterase 4B and gelsolin. Increased endocan mRNA levels in response to VEGF-A in endothelial cells and in human renal cancer have previously been reported. We now show increased endocan protein levels in VEGF-A treated endothelial cells and in human renal clear cell carcinoma. Increased protein expression was observed both in tumor cells and in a subset of tumor vessels, while expression in normal kidney tissue was low. VEGF-A seemed to be a specific inducer of endocan transcription since FGF-2, PDGF-BB, HGF/SF and EGF did not alter expression levels. Inhibition of PI3K with LY294002 caused a 12-fold increase in endocan transcription suggesting a repressive function of PI3K. In contrast inhibition of Src or MEK, which are signaling pathways activated by VEGF-A, did not influence basal or VEGF-A-induced endocan levels. In conclusion our study shows that, among angiogenic growth factors, VEGF-A is a specific inducer of endocan transcription which is translated into increased protein levels in VEGF-A treated endothelial cells. Increased endocan protein expression in human renal cancer suggests a role in tumor growth.
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Affiliation(s)
- Emma Rennel
- Department of Genetics and Pathology, the Rudbeck Laboratory, Uppsala University, S-751 85 Uppsala, Sweden
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Ameur A, Aurell E, Carlsson M, Westholm JO. Global gene expression analysis by combinatorial optimization. In Silico Biol 2004; 4:225-41. [PMID: 15107026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Generally, there is a trade-off between methods of gene expression analysis that are precise but labor-intensive, e.g. RT-PCR, and methods that scale up to global coverage but are not quite as quantitative, e.g. microarrays. In the present paper, we show how how a known method of gene expression profiling (K. Kato, Nucleic Acids Res. 23, 3685-3690 (1995)), which relies on a fairly small number of steps, can be turned into a global gene expression measurement by advanced data post-processing, with potentially little loss of accuracy. Post-processing here entails solving an ancillary combinatorial optimization problem. Validation is performed on in silico experiments generated from the FANTOM data base of full-length mouse cDNA. We present two variants of the method. One uses state-of-the-art commercial software for solving problems of this kind, the other a code developed by us specifically for this purpose, released in the public domain under GPL license.
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Affiliation(s)
- Adam Ameur
- SICS, Swedish Institute of Computer Science, P.O. Box 1263, S-164 29 Kista, Sweden
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