101
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Marzol E, Borassi C, Bringas M, Sede A, Rodríguez Garcia DR, Capece L, Estevez JM. Filling the Gaps to Solve the Extensin Puzzle. MOLECULAR PLANT 2018; 11:645-658. [PMID: 29530817 DOI: 10.1016/j.molp.2018.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/28/2018] [Accepted: 03/04/2018] [Indexed: 05/20/2023]
Abstract
Extensins (EXTs) are highly repetitive plant O-glycoproteins that require several post-translational modifications (PTMs) to become functional in plant cell walls. First, they are hydroxylated on contiguous proline residues; then they are O-glycosylated on hydroxyproline and serine. After secretion into the apoplast, O-glycosylated EXTs form a tridimensional network organized by inter- and intra-Tyr linkages. Recent studies have made significant progress in the identification of the enzymatic machinery required to process EXTs, which includes prolyl 4-hydroxylases, glycosyltransferases, papain-type cysteine endopeptidases, and peroxidases. EXTs are abundant in plant tissues and are particularly important in rapidly expanding root hairs and pollen tubes, which grow in a polar manner. Small changes in EXT PTMs affect fast-growing cells, although the molecular mechanisms underlying this regulation are unknown. In this review, we highlight recent advances in our understanding of EXT modifications throughout the secretory pathway, EXT assembly in cell walls, and possible sensing mechanisms involving the Catharanthus roseus cell surface sensor receptor-like kinases located at the interface between the apoplast and the cytoplasmic side of the plasma membrane.
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Affiliation(s)
- Eliana Marzol
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Cecilia Borassi
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (INQUIMAE-CONICET), Buenos Aires, CP C1428EGA, Argentina
| | - Ana Sede
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina; Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Dr. Héctor Torres (INGEBI-CONICET), Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina
| | - Diana Rosa Rodríguez Garcia
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (INQUIMAE-CONICET), Buenos Aires, CP C1428EGA, Argentina
| | - Jose M Estevez
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina.
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102
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Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity. Cell Metab 2018; 27:1121-1137.e5. [PMID: 29657031 PMCID: PMC5932137 DOI: 10.1016/j.cmet.2018.03.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/31/2018] [Accepted: 03/13/2018] [Indexed: 01/07/2023]
Abstract
Beige and brown adipocytes generate heat in response to reductions in ambient temperature. When warmed, both beige and brown adipocytes exhibit morphological "whitening," but it is unknown whether or to what extent this represents a true shift in cellular identity. Using cell-type-specific profiling in vivo, we uncover a unique paradigm of temperature-dependent epigenomic plasticity of beige, but not brown, adipocytes, with conversion from a brown to a white chromatin state. Despite this profound shift in cellular identity, warm whitened beige adipocytes retain an epigenomic memory of prior cold exposure defined by an array of poised enhancers that prime thermogenic genes for rapid response during a second bout of cold exposure. We further show that a transcriptional cascade involving glucocorticoid receptor and Zfp423 can drive warm-induced whitening of beige adipocytes. These studies identify the epigenomic and transcriptional bases of an extraordinary example of cellular plasticity in response to environmental signals.
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103
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Wang AW, Wangensteen KJ, Wang YJ, Zahm AM, Moss NG, Erez N, Kaestner KH. TRAP-seq identifies cystine/glutamate antiporter as a driver of recovery from liver injury. J Clin Invest 2018. [PMID: 29517978 DOI: 10.1172/jci95120] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding the molecular basis of the regenerative response following hepatic injury holds promise for improved treatment of liver diseases. Here, we report an innovative method to profile gene expression specifically in the hepatocytes that regenerate the liver following toxic injury. We used the Fah-/- mouse, a model of hereditary tyrosinemia, which conditionally undergoes severe liver injury unless fumarylacetoacetate hydrolase (FAH) expression is reconstituted ectopically. We used translating ribosome affinity purification followed by high-throughput RNA sequencing (TRAP-seq) to isolate mRNAs specific to repopulating hepatocytes. We uncovered upstream regulators and important signaling pathways that are highly enriched in genes changed in regenerating hepatocytes. Specifically, we found that glutathione metabolism, particularly the gene Slc7a11 encoding the cystine/glutamate antiporter (xCT), is massively upregulated during liver regeneration. Furthermore, we show that Slc7a11 overexpression in hepatocytes enhances, and its suppression inhibits, repopulation following toxic injury. TRAP-seq allows cell type-specific expression profiling in repopulating hepatocytes and identified xCT, a factor that supports antioxidant responses during liver regeneration. xCT has potential as a therapeutic target for enhancing liver regeneration in response to liver injury.
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Affiliation(s)
| | - Kirk J Wangensteen
- Department of Genetics and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Noam Erez
- Department of Genetics and.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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104
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Xie L, Yin A, Nichenko AS, Beedle AM, Call JA, Yin H. Transient HIF2A inhibition promotes satellite cell proliferation and muscle regeneration. J Clin Invest 2018. [PMID: 29533927 PMCID: PMC5983316 DOI: 10.1172/jci96208] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The remarkable regeneration capability of skeletal muscle depends on the coordinated proliferation and differentiation of satellite cells (SCs). The self-renewal of SCs is critical for long-term maintenance of muscle regeneration potential. Hypoxia profoundly affects the proliferation, differentiation, and self-renewal of cultured myoblasts. However, the physiological relevance of hypoxia and hypoxia signaling in SCs in vivo remains largely unknown. Here, we demonstrate that SCs are in an intrinsic hypoxic state in vivo and express hypoxia-inducible factor 2A (HIF2A). HIF2A promotes the stemness and long-term homeostatic maintenance of SCs by maintaining their quiescence, increasing their self-renewal, and blocking their myogenic differentiation. HIF2A stabilization in SCs cultured under normoxia augments their engraftment potential in regenerative muscle. Conversely, HIF2A ablation leads to the depletion of SCs and their consequent regenerative failure in the long-term. In contrast, transient pharmacological inhibition of HIF2A accelerates muscle regeneration by increasing SC proliferation and differentiation. Mechanistically, HIF2A induces the quiescence and self-renewal of SCs by binding the promoter of the Spry1 gene and activating Spry1 expression. These findings suggest that HIF2A is a pivotal mediator of hypoxia signaling in SCs and may be therapeutically targeted to improve muscle regeneration.
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Affiliation(s)
- Liwei Xie
- Department of Biochemistry and Molecular Biology.,Center for Molecular Medicine, and
| | - Amelia Yin
- Department of Biochemistry and Molecular Biology.,Center for Molecular Medicine, and
| | - Anna S Nichenko
- Department of Kinesiology, The University of Georgia, Athens, Georgia, USA
| | - Aaron M Beedle
- Department of Pharmaceutical Sciences, Binghamton University-SUNY, Binghamton, New York, USA
| | - Jarrod A Call
- Department of Kinesiology, The University of Georgia, Athens, Georgia, USA.,Regenerative Bioscience Center, The University of Georgia, Athens, Georgia, USA
| | - Hang Yin
- Department of Biochemistry and Molecular Biology.,Center for Molecular Medicine, and
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105
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Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R. A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nat Commun 2018; 9:1409. [PMID: 29651114 PMCID: PMC5897496 DOI: 10.1038/s41467-018-03851-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2018] [Indexed: 12/27/2022] Open
Abstract
Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
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Affiliation(s)
- Rahul Bhosale
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jitender Giri
- Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK.,National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Bipin K Pandey
- Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK.,National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Ricardo F H Giehl
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, OT Gatersleben, Stadt Seeland, Germany
| | - Anja Hartmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, OT Gatersleben, Stadt Seeland, Germany
| | - Richard Traini
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jekaterina Truskina
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK.,Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Nicola Leftley
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Meredith Hanlon
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
| | - Kamal Swarup
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Afaf Rashed
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Ute Voß
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jose Alonso
- Department of Plant and Microbial Biology, NC State University, Raleigh, NC 27695, USA
| | - Anna Stepanova
- Department of Plant and Microbial Biology, NC State University, Raleigh, NC 27695, USA
| | - Jeonga Yun
- Department of Plant and Microbial Biology, NC State University, Raleigh, NC 27695, USA
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Kathleen M Brown
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
| | - Jonathan P Lynch
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK.,Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Anthony Bishopp
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Darren Wells
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, OT Gatersleben, Stadt Seeland, Germany
| | - Malcolm J Bennett
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK. .,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK.
| | - Ranjan Swarup
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK. .,Centre for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, LE12 5RD, UK.
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106
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Kenyon A, Gavriouchkina D, Zorman J, Chong-Morrison V, Napolitani G, Cerundolo V, Sauka-Spengler T. Generation of a double binary transgenic zebrafish model to study myeloid gene regulation in response to oncogene activation in melanocytes. Dis Model Mech 2018; 11:dmm030056. [PMID: 29666124 PMCID: PMC5963855 DOI: 10.1242/dmm.030056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 02/01/2018] [Indexed: 12/11/2022] Open
Abstract
A complex network of inflammatory genes is closely linked to somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour, cancer cells have escaped the initial immune response mechanisms. Here, we describe the development of a double binary zebrafish model that enables regulatory programming of the myeloid cells as they respond to oncogene-activated melanocytes to be explored, focussing on the initial phase when cells become the precursors of cancer. A hormone-inducible binary system allows for temporal control of expression of different Ras oncogenes (NRasQ61K, HRasG12V and KRasG12V) in melanocytes, leading to proliferation and changes in morphology of the melanocytes. This model was coupled to binary cell-specific biotagging models allowing in vivo biotinylation and subsequent isolation of macrophage or neutrophil nuclei for regulatory profiling of their active transcriptomes. Nuclear transcriptional profiling of neutrophils, performed as they respond to the earliest precursors of melanoma in vivo, revealed an intricate landscape of regulatory factors that may promote progression to melanoma, including Serpinb1l4, Fgf1, Fgf6, Cathepsin H, Galectin 1 and Galectin 3. The model presented here provides a powerful platform to study the myeloid response to the earliest precursors of melanoma.
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Affiliation(s)
- Amy Kenyon
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Daria Gavriouchkina
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Jernej Zorman
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Vanessa Chong-Morrison
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Giorgio Napolitani
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Vincenzo Cerundolo
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Tatjana Sauka-Spengler
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
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107
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Reynoso MA, Pauluzzi GC, Cabanlit S, Velasco J, Bazin J, Deal R, Brady S, Sinha N, Bailey-Serres J, Kajala K. Isolation of Nuclei in Tagged Cell Types (INTACT), RNA Extraction and Ribosomal RNA Degradation to Prepare Material for RNA-Seq. Bio Protoc 2018; 8:e2458. [PMID: 34286007 DOI: 10.21769/bioprotoc.2458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 11/02/2022] Open
Abstract
Gene expression is dynamically regulated on many levels, including chromatin accessibility and transcription. In order to study these nuclear regulatory events, we describe our method to purify nuclei with Isolation of Nuclei in TAgged Cell Types (INTACT). As nuclear RNA is low in polyadenylated transcripts and conventional pulldown methods would not capture non-polyadenylated pre-mRNA, we also present our method to remove ribosomal RNA from the total nuclear RNA in preparation for nuclear RNA-Seq.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Jérémie Bazin
- IPS2, Institute of Plant Science-Paris Saclay (CNRS-INRA), University of Paris-Saclay, Orsay, France
| | | | - Siobhan Brady
- Department of Plant Biology, UC Davis, Davis, CA, USA.,Genome Center, UC Davis, Davis, CA, USA
| | - Neelima Sinha
- Department of Plant Biology, UC Davis, Davis, CA, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Kaisa Kajala
- Department of Plant Biology, UC Davis, Davis, CA, USA.,Genome Center, UC Davis, Davis, CA, USA
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108
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Sijacic P, Bajic M, McKinney EC, Meagher RB, Deal RB. Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94. [PMID: 29513366 PMCID: PMC7219318 DOI: 10.1111/tpj.13882] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cell differentiation is driven by changes in the activity of transcription factors (TFs) and subsequent alterations in transcription. To study this process, differences in TF binding between cell types can be deduced by probing chromatin accessibility. We used cell type-specific nuclear purification followed by the assay for transposase-accessible chromatin (ATAC-seq) to delineate differences in chromatin accessibility and TF regulatory networks between stem cells of the shoot apical meristem (SAM) and differentiated leaf mesophyll cells in Arabidopsis thaliana. Chromatin accessibility profiles of SAM stem cells and leaf mesophyll cells were very similar at a qualitative level, yet thousands of regions having quantitatively different chromatin accessibility were also identified. Analysis of the genomic regions preferentially accessible in each cell type identified hundreds of overrepresented TF-binding motifs, highlighting sets of TFs that are probably important for each cell type. Within these sets, we found evidence for extensive co-regulation of target genes by multiple TFs that are preferentially expressed in each cell type. Interestingly, the TFs within each of these cell type-enriched sets also showed evidence of extensively co-regulating each other. We further found that preferentially accessible chromatin regions in mesophyll cells tended to also be substantially accessible in the stem cells, whereas the converse was not true. This observation suggests that the generally higher accessibility of regulatory elements in stem cells might contribute to their developmental plasticity. This work demonstrates the utility of cell type-specific chromatin accessibility profiling for the rapid development of testable models of regulatory control differences between cell types.
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Affiliation(s)
- Paja Sijacic
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, GA 30322
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322
| | | | | | - Roger B. Deal
- Department of Biology, Emory University, Atlanta, GA 30322
- Correspondence to: Roger B. Deal;
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109
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McCormick S. Assessing transcriptional network changes accompanying cell differentiation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:213-214. [PMID: 29607590 DOI: 10.1111/tpj.13912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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110
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Lee TA, Bailey-Serres J. Lighting the shadows: methods that expose nuclear and cytoplasmic gene regulatory control. Curr Opin Biotechnol 2018; 49:29-34. [DOI: 10.1016/j.copbio.2017.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
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111
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The Expanding Toolkit of Translating Ribosome Affinity Purification. J Neurosci 2018; 37:12079-12087. [PMID: 29237735 DOI: 10.1523/jneurosci.1929-17.2017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/16/2017] [Accepted: 11/03/2017] [Indexed: 01/23/2023] Open
Abstract
Translating ribosome affinity purification is a method initially developed for profiling mRNA from genetically defined cell types in complex tissues. It has been applied both to identify target molecules in cell types that are important for controlling a variety of behaviors in the brain, and to understand the molecular consequences on those cells due to experimental manipulations, ranging from drugs of abuse to disease-causing mutations. Since its inception, a variety of methodological advances are opening new avenues of investigation. These advances include a variety of new methods for targeting cells for translating ribosome affinity purification by features such as their projections or activity, additional tags and mouse reagents increasing the flexibility of the system, and new modifications of the method specifically focused on studying the regulation of translation. The latter includes methods to assess cell type-specific regulation of translation in specific subcellular compartments. Here, I provide a summary of these recent advances and resources, highlighting both new experimental opportunities and areas for future technical development.
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112
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Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB. Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. THE PLANT CELL 2018. [PMID: 29229750 DOI: 10.1101/167932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the assay for transposase-accessible chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell-type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell-type-specific transcriptomes during development.
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Affiliation(s)
- Kelsey A Maher
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mauricio Reynoso
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Germain Pauluzzi
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Margaret Woodhouse
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kerry Bubb
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Michael W Dorrity
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Christine Queitsch
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
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113
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Reynoso MA, Pauluzzi GC, Kajala K, Cabanlit S, Velasco J, Bazin J, Deal R, Sinha NR, Brady SM, Bailey-Serres J. Nuclear Transcriptomes at High Resolution Using Retooled INTACT. PLANT PHYSIOLOGY 2018; 176:270-281. [PMID: 28956755 PMCID: PMC5761756 DOI: 10.1104/pp.17.00688] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/26/2017] [Indexed: 05/03/2023]
Abstract
Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here, we describe transfer of the isolation of nuclei from tagged specific cell types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear-envelope-targeting domain of the nuclear tagging fusion (NTF) protein with an outer nuclear-envelope-anchored domain. This modified NTF was combined with codon-optimized Escherichia coli BirA in a single T-DNA construct. We also developed inexpensive methods for INTACT, T-DNA insertion mapping, and profiling of the complete nuclear transcriptome, including a ribosomal RNA degradation procedure that minimizes pre-ribosomal RNA (pre-rRNA) transcripts. A high-resolution comparison of nuclear and steady-state poly(A)+ transcript populations of seedling root tips confirmed the capture of pre-messenger RNA (pre-mRNA) and exposed distinctions in diversity and abundance of the nuclear and total transcriptomes. This retooled INTACT can enable high-resolution monitoring of the nuclear transcriptome and chromatin in specific cell types of rice and other species.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Kaisa Kajala
- Department of Plant Biology, University of California, Davis, California 95616
- Genome Center, University of California, Davis, California 95616
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Jérémie Bazin
- IPS2, Institute of Plant Science-Paris Saclay (CNRS-INRA), University of Paris-Saclay, F-911405, Orsay, France
| | - Roger Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, California 95616
- Genome Center, University of California, Davis, California 95616
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
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114
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Roux B, Rodde N, Moreau S, Jardinaud MF, Gamas P. Laser Capture Micro-Dissection Coupled to RNA Sequencing: A Powerful Approach Applied to the Model Legume Medicago truncatula in Interaction with Sinorhizobium meliloti. Methods Mol Biol 2018; 1830:191-224. [PMID: 30043372 DOI: 10.1007/978-1-4939-8657-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Understanding the development of multicellular organisms requires the identification of regulators, notably transcription factors, and specific transcript populations associated with tissue differentiation. Laser capture microdissection (LCM) is one of the techniques that enable the analysis of distinct tissues or cells within an organ. Coupling this technique with RNA sequencing (RNAseq) makes it extremely powerful to obtain a genome-wide and dynamic view of gene expression. Moreover, RNA sequencing allows two or potentially more interacting organisms to be analyzed simultaneously. In this chapter, a LCM-RNAseq protocol optimized for root and symbiotic root nodule analysis is presented, using the model legume Medicago truncatula (in interaction with Sinorhizobium meliloti in the nodule samples). This includes the description of procedures for plant material fixation, embedding, and micro-dissection; it is followed by a presentation of techniques for RNA extraction and amplification, adapted for the simultaneous analysis of plant and bacterial cells in interaction or, more generally, polyadenylated and non-polyadenylated RNAs. Finally, step-by-step statistical analyses of RNAseq data are described. Those are critical for quality assessment of the whole procedure and for the identification of differentially expressed genes.
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Affiliation(s)
- Brice Roux
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- BIAM, Université Aix-Marseille, CNRS, CEA, Saint-Paul-lez-Durance, France
| | - Nathalie Rodde
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- CNRGV, INRA, Castanet-Tolosan, France
| | - Sandra Moreau
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marie-Françoise Jardinaud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- INPT-Université de Toulouse, ENSAT, Castanet-Tolosan, France
| | - Pascal Gamas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
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115
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Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity MW, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal RB. Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. THE PLANT CELL 2018; 30:15-36. [PMID: 29229750 PMCID: PMC5810565 DOI: 10.1105/tpc.17.00581] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/30/2017] [Accepted: 12/06/2017] [Indexed: 05/19/2023]
Abstract
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the assay for transposase-accessible chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell-type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell-type-specific transcriptomes during development.
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Affiliation(s)
- Kelsey A Maher
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, Georgia 30322
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia 30322
| | - Kaisa Kajala
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mauricio Reynoso
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Germain Pauluzzi
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Donnelly A West
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Margaret Woodhouse
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kerry Bubb
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Michael W Dorrity
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Christine Queitsch
- University of Washington, School of Medicine, Department of Genome Sciences, Seattle, Washington 98195
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
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Pirrello J, Deluche C, Frangne N, Gévaudant F, Maza E, Djari A, Bourge M, Renaudin JP, Brown S, Bowler C, Zouine M, Chevalier C, Gonzalez N. Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:387-398. [PMID: 29172253 DOI: 10.1111/tpj.13783] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
As part of normal development most eukaryotic organisms, ranging from insects and mammals to plants, display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene-specific ploidy-regulated transcription remains open. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA sequencing (RNA-Seq) approach using total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei based on their DNA content. Here we show that cell-based approaches to the study of RNA-Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy-specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location.
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Affiliation(s)
- Julien Pirrello
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | - Cynthia Deluche
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
| | - Nathalie Frangne
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
| | - Frédéric Gévaudant
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
| | - Elie Maza
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | - Anis Djari
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | - Mickaël Bourge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | | | - Spencer Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Chris Bowler
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Mohamed Zouine
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | | | - Nathalie Gonzalez
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
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117
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Tannenbaum M, Sarusi-Portuguez A, Krispil R, Schwartz M, Loza O, Benichou JIC, Mosquna A, Hakim O. Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq. PLANT METHODS 2018; 14:113. [PMID: 30598689 PMCID: PMC6300899 DOI: 10.1186/s13007-018-0381-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/10/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana and define organ-specific regulatory sites and binding motifs of TFs at these sites. RESULTS We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel gene-distant regulatory elements. CONCLUSIONS By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
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Affiliation(s)
- Miriam Tannenbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avital Sarusi-Portuguez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Ronen Krispil
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jennifer I. C. Benichou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Assaf Mosquna
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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118
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Morao AK, Caillieux E, Colot V, Roudier F. Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins. Methods Mol Biol 2018; 1675:111-130. [PMID: 29052189 DOI: 10.1007/978-1-4939-7318-7_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Progression of a cell along a differentiation path is characterized by changes in gene expression profiles. Alterations of these transcriptional programs result from cell type-specific transcription factors that act in a dynamic chromatin environment. Understanding the precise contribution of these molecular factors during the differentiation process requires accessing specific cell types within a developing organ. This chapter describes a streamlined and alternative version of INTACT, a method enabling the isolation of specific cell populations by affinity-purification of tagged nuclei and the subsequent analysis of gene expression, transcription factor binding profiles, as well as chromatin state at a genome-wide scale. In particular, modifications of the nuclei isolation, capture, and purification procedures are proposed that improve time scale, yield, and purity. In addition, the combination of different tags enables the analysis of distinct cell populations from a single transgenic line and the subtractive purification of subpopulations of cells, including those for which no specific promoter is available. Finally, we describe a chromatin immunoprecipitation protocol that has been successfully used to profile histone modifications and other chromatin-associated proteins such as RNA Polymerase II in different cell populations of the Arabidopsis root, including the quiescent center of the stem cell niche.
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Affiliation(s)
- Ana Karina Morao
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - Erwann Caillieux
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - Vincent Colot
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - François Roudier
- Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France.
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France.
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119
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Abstract
Identifying and characterizing highly accessible chromatin regions assists in determining the location of genomic regulatory elements and understanding transcriptional regulation. In this chapter, we describe an approach to map accessible chromatin features in plants using the Assay for Transposase-Accessible Chromatin, combined with high-throughput sequencing (ATAC-seq), which was originally developed for cultured animal cells. This technique utilizes a hyperactive Tn5 transposase to cause DNA cleavage and simultaneous insertion of sequencing adapters into open chromatin regions of the input nuclei. The application of ATAC-seq to plant tissue has been challenging due to the difficulty of isolating nuclei sufficiently free of interfering organellar DNA. Here we present two different approaches to purify plant nuclei for ATAC-seq: the INTACT method (Isolation of Nuclei TAgged in specific Cell Types) to isolate nuclei from individual cell types of the plant, and tissue lysis followed by sucrose sedimentation to isolate sufficiently pure total nuclei. We provide detailed instructions for transposase treatment of nuclei isolated using either approach, as well as subsequent preparation of ATAC-seq libraries. Sequencing-ready ATAC-seq libraries can be prepared from plant tissue in as little as one day. The procedures described here are optimized for Arabidopsis thaliana but can also be applied to other plant species.
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120
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Roh HC, Tsai LTY, Lyubetskaya A, Tenen D, Kumari M, Rosen ED. Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo. Cell Rep 2017; 18:1048-1061. [PMID: 28122230 DOI: 10.1016/j.celrep.2016.12.087] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/28/2016] [Accepted: 12/27/2016] [Indexed: 12/31/2022] Open
Abstract
Epigenomic mechanisms direct distinct gene expression programs for different cell types. Various in vivo tissues have been subjected to epigenomic analysis; however, these studies have been limited by cellular heterogeneity, resulting in composite gene expression and epigenomic profiles. Here, we introduce "NuTRAP," a transgenic mouse that allows simultaneous isolation of cell-type-specific translating mRNA and chromatin from complex tissues. Using NuTRAP, we successfully characterize gene expression and epigenomic states of various adipocyte populations in vivo, revealing significant differences compared to either whole adipose tissue or in vitro adipocyte cell lines. We find that chromatin immunoprecipitation sequencing (ChIP-seq) using NuTRAP is highly efficient, scalable, and robust with even limited cell input. We further demonstrate the general utility of NuTRAP by analyzing hepatocyte-specific epigenomic states. The NuTRAP mouse is a resource that provides a powerful system for cell-type-specific gene expression and epigenomic profiling.
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Affiliation(s)
- Hyun Cheol Roh
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Linus T-Y Tsai
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Anna Lyubetskaya
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Danielle Tenen
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Manju Kumari
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Evan D Rosen
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02142, USA.
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121
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Palovaara J, Saiga S, Wendrich JR, van 't Wout Hofland N, van Schayck JP, Hater F, Mutte S, Sjollema J, Boekschoten M, Hooiveld GJ, Weijers D. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS 2017; 3:894-904. [PMID: 29116234 PMCID: PMC5687563 DOI: 10.1038/s41477-017-0035-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | | | - J Paul van Schayck
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Friederike Hater
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jouke Sjollema
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Mark Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Guido J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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122
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Palovaara J, Saiga S, Wendrich JR, van 't Wout Hofland N, van Schayck JP, Hater F, Mutte S, Sjollema J, Boekschoten M, Hooiveld GJ, Weijers D. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS 2017; 3:894-904. [PMID: 29116234 DOI: 10.1038/s41477-017-0035-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/22/2023]
Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | | | - J Paul van Schayck
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Friederike Hater
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jouke Sjollema
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Mark Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Guido J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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Chica C, Louis A, Roest Crollius H, Colot V, Roudier F. Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation. Genome Biol 2017; 18:207. [PMID: 29084582 PMCID: PMC5663038 DOI: 10.1186/s13059-017-1333-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 10/03/2017] [Indexed: 01/05/2023] Open
Abstract
Background Polycomb Repressive Complexes 2 (PRC2) are multi-protein chromatin modifiers that are evolutionarily conserved among eukaryotes and play key roles in the regulation of gene expression, notably through the trimethylation of lysine 27 of histone H3 (H3K27me3). Although PRC2-mediated gene regulation has been studied in many organisms, few studies have explored in depth the evolutionary conservation of PRC2 targets. Results Here, we compare the H3K27me3 epigenomic profiles for the two closely related species Arabidopsis thaliana and Arabidopsis lyrata and the more distant species Arabis alpina, three Brassicaceae that diverged from each other within the past 24 million years. Using a robust set of gene orthologs present in the three species, we identify two classes of evolutionarily conserved PRC2 targets, which are characterized by either developmentally plastic or developmentally constrained H3K27me3 marking across species. Constrained H3K27me3 marking is associated with higher conservation of promoter sequence information content and higher nucleosome occupancy compared to plastic H3K27me3 marking. Moreover, gene orthologs with constrained H3K27me3 marking exhibit a higher degree of tissue specificity and tend to be involved in developmental functions, whereas gene orthologs with plastic H3K27me3 marking preferentially encode proteins associated with metabolism and stress responses. In addition, gene orthologs with constrained H3K27me3 marking are the predominant contributors to higher-order chromosome organization. Conclusions Our findings indicate that developmentally plastic and constrained H3K27me3 marking define two evolutionarily conserved modes of PRC2-mediated gene regulation that are associated with distinct selective pressures operating at multiple scales, from DNA sequence to gene function and chromosome architecture. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1333-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudia Chica
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, F-75005, France.,Present address: Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, F-75005, France
| | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, F-75005, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, F-75005, France.
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, F-75005, France. .,Present address: Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France.
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124
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Galbraith DW, Sliwinska E, Samadder P. Nuclear Cytometry: Analysis of the Patterns of DNA Synthesis and Transcription Using Flow Cytometry, Confocal Microscopy, and RNA Sequencing. Methods Mol Biol 2017; 1678:371-392. [PMID: 29071687 DOI: 10.1007/978-1-4939-7346-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Eukaryotes are defined by cells that contain a nucleus and other membrane-bound organelles. Cytometric analysis in situ, utilizing imaging, provides a useful understanding of the structure and function of the various subcellular components, particularly when combined with methods that preserve the living state. In terms of information provided by the observation of eukaryotic nuclei, imaging has provided a wealth of information about cellular multiplication. When organisms are present in multicellular form (tissues and organs), this property does not generally confound imaging cytometry. Multicellular eukaryotic species present immediate problems when being considered for analysis using flow cytometry which requires suspensions of single particles. Although some eukaryotic cell types exist as natural single cell suspensions (cf. the erythropoietic system), for other tissues and organs, strategies are required to produce single particle suspensions. This chapter illustrates the application of flow cytometry combined with confocal microscopy to analyze complex organs, focusing on properties of the plant nucleus, and then goes on to describe how suspensions of nuclei can be prepared from tissues and organs, and used for flow cytometric analysis of cellular and transcriptional states. The application of these techniques to animal species is also discussed with the implication that this strategy is universally applicable for the characterization of nuclei within tissues that cannot readily be converted into suspensions of cells.
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Affiliation(s)
- David W Galbraith
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA.
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Plant Genetics, Physiology and Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Partha Samadder
- School of Plant Sciences, Bio5 Institute, University of Arizona, 341 Keating Building, 1657 E. Helen Street, Tucson, AZ, 85721, USA
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125
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Abstract
Dynamic reshuffling of the chromatin landscape is a recurrent theme orchestrated in many, if not all, plant developmental transitions and adaptive responses. Spatiotemporal variations of the chromatin properties on regulatory genes and on structural genomic elements trigger the establishment of distinct transcriptional contexts, which in some instances can epigenetically be inherited. Studies on plant cell plasticity during the differentiation of stem cells, including gametogenesis, or the specialization of vegetative cells in various organs, as well as the investigation of allele-specific gene regulation have long been impaired by technical challenges in generating specific chromatin profiles in complex or hardly accessible cell populations. Recent advances in increasing the sensitivity of genome-enabled technologies and in the isolation of specific cell types have allowed for overcoming such limitations. These developments hint at multilevel regulatory events ranging from nucleosome accessibility and composition to higher order chromatin organization and genome topology. Uncovering the large extent to which chromatin dynamics and epigenetic processes influence gene expression is therefore not surprisingly revolutionizing current views on plant molecular genetics and (epi)genomics as well as their perspectives in eco-evolutionary biology. Here, we introduce current methodologies to probe genome-wide chromatin variations for which protocols are detailed in this book chapter, with an emphasis on the plant model species Arabidopsis.
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126
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Christopher MA, Kyle SM, Katz DJ. Neuroepigenetic mechanisms in disease. Epigenetics Chromatin 2017; 10:47. [PMID: 29037228 PMCID: PMC5644115 DOI: 10.1186/s13072-017-0150-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/23/2017] [Indexed: 02/08/2023] Open
Abstract
Epigenetics allows for the inheritance of information in cellular lineages during differentiation, independent of changes to the underlying genetic sequence. This raises the question of whether epigenetic mechanisms also function in post-mitotic neurons. During the long life of the neuron, fluctuations in gene expression allow the cell to pass through stages of differentiation, modulate synaptic activity in response to environmental cues, and fortify the cell through age-related neuroprotective pathways. Emerging evidence suggests that epigenetic mechanisms such as DNA methylation and histone modification permit these dynamic changes in gene expression throughout the life of a neuron. Accordingly, recent studies have revealed the vital importance of epigenetic players in the central nervous system and during neurodegeneration. Here, we provide a review of several of these recent findings, highlighting novel functions for epigenetics in the fields of Rett syndrome, Fragile X syndrome, and Alzheimer’s disease research. Together, these discoveries underscore the vital importance of epigenetics in human neurological disorders.
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Affiliation(s)
- Michael A Christopher
- Department of Cell Biology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA, 30322, USA.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095-7239, USA
| | - Stephanie M Kyle
- Department of Cell Biology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA, 30322, USA
| | - David J Katz
- Department of Cell Biology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA, 30322, USA.
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127
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Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem. Proc Natl Acad Sci U S A 2017; 114:E8922-E8929. [PMID: 28973915 DOI: 10.1073/pnas.1707400114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem, a group of slowly dividing quiescent center cells is thought to limit stem cell activity to directly neighboring cells, thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction to the more gradual changes in cell division potential and differentiation that occur as cells move further away from the quiescent center. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from stem cell activity toward differentiation.
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128
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Kanca O, Bellen HJ, Schnorrer F. Gene Tagging Strategies To Assess Protein Expression, Localization, and Function in Drosophila. Genetics 2017; 207:389-412. [PMID: 28978772 PMCID: PMC5629313 DOI: 10.1534/genetics.117.199968] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/13/2017] [Indexed: 01/15/2023] Open
Abstract
Analysis of gene function in complex organisms relies extensively on tools to detect the cellular and subcellular localization of gene products, especially proteins. Typically, immunostaining with antibodies provides these data. However, due to cost, time, and labor limitations, generating specific antibodies against all proteins of a complex organism is not feasible. Furthermore, antibodies do not enable live imaging studies of protein dynamics. Hence, tagging genes with standardized immunoepitopes or fluorescent tags that permit live imaging has become popular. Importantly, tagging genes present in large genomic clones or at their endogenous locus often reports proper expression, subcellular localization, and dynamics of the encoded protein. Moreover, these tagging approaches allow the generation of elegant protein removal strategies, standardization of visualization protocols, and permit protein interaction studies using mass spectrometry. Here, we summarize available genomic resources and techniques to tag genes and discuss relevant applications that are rarely, if at all, possible with antibodies.
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Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030
- Howard Hughes Medical Institute, Houston, Texas 77030
| | - Frank Schnorrer
- Developmental Biology Institute of Marseille (IBDM), UMR 7288, CNRS, Aix-Marseille Université, 13288, France
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129
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Johnson B, Zhao Y, Fasolino M, Lamonica J, Kim Y, Georgakilas G, Wood K, Bu D, Cui Y, Goffin D, Vahedi G, Kim T, Zhou Z. Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome. Nat Med 2017; 23:1203-1214. [PMID: 28920956 PMCID: PMC5630512 DOI: 10.1038/nm.4406] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/18/2017] [Indexed: 12/12/2022]
Abstract
Mutations in MECP2 cause Rett syndrome (RTT), an X-linked neurological disorder characterized by regressive loss of neurodevelopmental milestones and acquired psychomotor deficits. However, the cellular heterogeneity of the brain impedes an understanding of how MECP2 mutations contribute to RTT. Here we developed a Cre-inducible method for cell-type-specific biotin tagging of MeCP2 in mice. Combining this approach with an allelic series of knock-in mice carrying frequent RTT-associated mutations (encoding T158M and R106W) enabled the selective profiling of RTT-associated nuclear transcriptomes in excitatory and inhibitory cortical neurons. We found that most gene-expression changes were largely specific to each RTT-associated mutation and cell type. Lowly expressed cell-type-enriched genes were preferentially disrupted by MeCP2 mutations, with upregulated and downregulated genes reflecting distinct functional categories. Subcellular RNA analysis in MeCP2-mutant neurons further revealed reductions in the nascent transcription of long genes and uncovered widespread post-transcriptional compensation at the cellular level. Finally, we overcame X-linked cellular mosaicism in female RTT models and identified distinct gene-expression changes between neighboring wild-type and mutant neurons, providing contextual insights into RTT etiology that support personalized therapeutic interventions.
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Affiliation(s)
- B.S. Johnson
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Y.T. Zhao
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - M. Fasolino
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - J.M. Lamonica
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Y.J. Kim
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - G. Georgakilas
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - K.H. Wood
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - D. Bu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Y. Cui
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - D. Goffin
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - G. Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - T.H. Kim
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Z. Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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130
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Qiao Z, Pingault L, Zogli P, Langevin M, Rech N, Farmer A, Libault M. A comparative genomic and transcriptomic analysis at the level of isolated root hair cells reveals new conserved root hair regulatory elements. PLANT MOLECULAR BIOLOGY 2017; 94:641-655. [PMID: 28687904 DOI: 10.1007/s11103-017-0630-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE A comparative transcriptomic and genomic analysis between Arabidopsis thaliana and Glycine max root hair genes reveals the evolution of the expression of plant genes after speciation and whole genome duplication. Our understanding of the conservation and divergence of the expression patterns of genes between plant species is limited by the quality of the genomic and transcriptomic resources available. Specifically, the transcriptomes generated from plant organs are the reflection of the contribution of the different cell types composing the samples weighted by their relative abundances in the sample. These contributions can vary between plant species leading to the generation of datasets which are difficult to compare. To gain a deeper understanding of the evolution of gene transcription in and between plant species, we performed a comparative transcriptomic and genomic analysis at the level of one single plant cell type, the root hair cell, and between two model plants: Arabidopsis (Arabidopsis thaliana) and soybean (Glycine max). These two species, which diverged 90 million years ago, were selected as models based on the large amount of genomic and root hair transcriptomic information currently available. Our analysis revealed in detail the transcriptional divergence and conservation between soybean paralogs (i.e., the soybean genome is the product of two successive whole genome duplications) and between Arabidopsis and soybean orthologs in this single plant cell type. Taking advantage of this evolutionary study, we combined bioinformatics, molecular, cellular and microscopic tools to characterize plant promoter sequences and the discovery of two root hair regulatory elements (RHE1 and RHE2) consistently and specifically active in plant root hair cells.
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Affiliation(s)
- Zhenzhen Qiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Lise Pingault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Prince Zogli
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Micaela Langevin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Niccole Rech
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Marc Libault
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
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131
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Foley SW, Kramer MC, Gregory BD. RNA structure, binding, and coordination in Arabidopsis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28660659 DOI: 10.1002/wrna.1426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/08/2017] [Accepted: 04/13/2017] [Indexed: 11/05/2022]
Abstract
From the moment of transcription, up through degradation, each RNA transcript is bound by an ever-changing cohort of RNA binding proteins. The binding of these proteins is regulated by both the primary RNA sequence, as well as the intramolecular RNA folding, or secondary structure, of the transcript. Thus, RNA secondary structure regulates many post-transcriptional processes. With the advent of next generation sequencing, several techniques have been developed to generate global landscapes of both RNA-protein interactions and RNA secondary structure. In this review, we describe the current state of the field detailing techniques to globally interrogate RNA secondary structure and/or RNA-protein interaction sites, as well as our current understanding of these features in the transcriptome of the model plant Arabidopsis thaliana. WIREs RNA 2017, 8:e1426. doi: 10.1002/wrna.1426 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Shawn W Foley
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Marianne C Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
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132
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Kubota A, Ito S, Shim JS, Johnson RS, Song YH, Breton G, Goralogia GS, Kwon MS, Laboy Cintrón D, Koyama T, Ohme-Takagi M, Pruneda-Paz JL, Kay SA, MacCoss MJ, Imaizumi T. TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLoS Genet 2017. [PMID: 28628608 PMCID: PMC5495492 DOI: 10.1371/journal.pgen.1006856] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Photoperiod is one of the most reliable environmental cues for plants to regulate flowering timing. In Arabidopsis thaliana, CONSTANS (CO) transcription factor plays a central role in regulating photoperiodic flowering. In contrast to posttranslational regulation of CO protein, still little was known about CO transcriptional regulation. Here we show that the CINCINNATA (CIN) clade of class II TEOSINTE BRANCHED 1/ CYCLOIDEA/ PROLIFERATING CELL NUCLEAR ANTIGEN FACTOR (TCP) proteins act as CO activators. Our yeast one-hybrid analysis revealed that class II CIN-TCPs, including TCP4, bind to the CO promoter. TCP4 induces CO expression around dusk by directly associating with the CO promoter in vivo. In addition, TCP4 binds to another flowering regulator, GIGANTEA (GI), in the nucleus, and induces CO expression in a GI-dependent manner. The physical association of TCP4 with the CO promoter was reduced in the gi mutant, suggesting that GI may enhance the DNA-binding ability of TCP4. Our tandem affinity purification coupled with mass spectrometry (TAP-MS) analysis identified all class II CIN-TCPs as the components of the in vivo TCP4 complex, and the gi mutant did not alter the composition of the TCP4 complex. Taken together, our results demonstrate a novel function of CIN-TCPs as photoperiodic flowering regulators, which may contribute to coordinating plant development with flowering regulation. For plant adaptation to seasonal environments, a crucial developmental event is flowering, as proper timing of flowering affects reproductive success. Although plants monitor various environmental parameters to optimize this timing, photoperiod information is important for plants to regulate seasonal flowering time, because changes in photoperiod occur in a predictable manner throughout the year. The model plant Arabidopsis thaliana responds to photoperiodic changes and flowers under long-day conditions. Based on genetic analyses using mutants defective in the photoperiodic flowering response, we learned that the transcription factor referred to as CONSTANS (CO) plays a central role in regulating the timing of flowering by directly controlling the expression of florigen (flowering-inducing substrate) gene. Long-day afternoon expression of CO is critical for this regulation; however, we had limited knowledge of CO transcriptional regulation. Here we identified that a group of plant-specific transcription factors belonging to the TCP gene family function as novel CO transcriptional activators. We demonstrated that TCP transcription factors regulate CO transcription together with known regulators of CO. Our results imply that plants utilize multiple transcription factors to precisely coordinate the expression of the key regulator gene, CO, which will directly affect flowering time.
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Affiliation(s)
- Akane Kubota
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Shogo Ito
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Jae Sung Shim
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Yong Hun Song
- Department of Life Sciences, Ajou University, Suwon, Korea
| | - Ghislain Breton
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Greg S. Goralogia
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Michael S. Kwon
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Dianne Laboy Cintrón
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Tomotsugu Koyama
- Bioorganic Research Center, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Masaru Ohme-Takagi
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Jose L. Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Steve A. Kay
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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133
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You Y, Sawikowska A, Neumann M, Posé D, Capovilla G, Langenecker T, Neher RA, Krajewski P, Schmid M. Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. Nat Commun 2017; 8:15120. [PMID: 28513600 PMCID: PMC5442315 DOI: 10.1038/ncomms15120] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 03/01/2017] [Indexed: 02/04/2023] Open
Abstract
Plants can produce organs throughout their entire life from pluripotent stem cells located at their growing tip, the shoot apical meristem (SAM). At the time of flowering, the SAM of Arabidopsis thaliana switches fate and starts producing flowers instead of leaves. Correct timing of flowering in part determines reproductive success, and is therefore under environmental and endogenous control. How epigenetic regulation contributes to the floral transition has eluded analysis so far, mostly because of the poor accessibility of the SAM. Here we report the temporal dynamics of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with transcriptional changes at the SAM in response to photoperiod-induced flowering. Emphasizing the importance of tissue-specific epigenomic analyses we detect enrichments of chromatin states in the SAM that were not apparent in whole seedlings. Furthermore, our results suggest that regulation of translation might be involved in adjusting meristem function during the induction of flowering. When plants flower, the shoot apical meristem switches fate to produce floral organs instead of leaves. Here You et al. perform tissue-specific epigenome profiling and show that during this transition changes in histone methylation are correlated with transcriptional responses in the meristem.
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Affiliation(s)
- Yuan You
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Aneta Sawikowska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - David Posé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Giovanna Capovilla
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Tobias Langenecker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Richard A Neher
- Evolutionary Dynamics and Biophysics Group, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.,Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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134
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Tulisiak CT, Harris RA, Ponomarev I. DNA modifications in models of alcohol use disorders. Alcohol 2017; 60:19-30. [PMID: 27865607 DOI: 10.1016/j.alcohol.2016.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/03/2016] [Accepted: 11/05/2016] [Indexed: 02/07/2023]
Abstract
Chronic alcohol use and abuse result in widespread changes to gene expression, some of which contribute to the development of alcohol-use disorders (AUD). Gene expression is controlled, in part, by a group of regulatory systems often referred to as epigenetic factors, which includes, among other mechanisms, chemical marks made on the histone proteins around which genomic DNA is wound to form chromatin, and on nucleotides of the DNA itself. In particular, alcohol has been shown to perturb the epigenetic machinery, leading to changes in gene expression and cellular functions characteristic of AUD and, ultimately, to altered behavior. DNA modifications in particular are seeing increasing research in the context of alcohol use and abuse. To date, studies of DNA modifications in AUD have primarily looked at global methylation profiles in human brain and blood, gene-specific methylation profiles in animal models, methylation changes associated with prenatal ethanol exposure, and the potential therapeutic abilities of DNA methyltransferase inhibitors. Future studies may be aimed at identifying changes to more recently discovered DNA modifications, utilizing new methods to discriminate methylation profiles between cell types, thus clarifying how alcohol influences the methylomes of cell-type populations and how this may affect downstream processes. These studies and more in-depth probing of DNA methylation will be key to determining whether DNA-level epigenetic regulation plays a causative role in AUD and can thus be targeted for treatment of the disorder.
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Affiliation(s)
- Christopher T Tulisiak
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA; The College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, A1900, Austin, TX 78712, USA
| | - Igor Ponomarev
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA; The College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, A1900, Austin, TX 78712, USA.
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135
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Trinh LA, Chong-Morrison V, Gavriouchkina D, Hochgreb-Hägele T, Senanayake U, Fraser SE, Sauka-Spengler T. Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Rep 2017; 19:425-440. [PMID: 28402863 PMCID: PMC5400779 DOI: 10.1016/j.celrep.2017.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/21/2016] [Accepted: 03/13/2017] [Indexed: 11/22/2022] Open
Abstract
Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types and robust methods for biochemical profiling of target proteins. We have developed a versatile, tissue-specific binary in vivo biotinylation system in zebrafish termed biotagging that uses genetically encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific drivers and cell-compartment-specific effector lines, we demonstrate the specificity of the biotagging toolkit at the biochemical, cellular, and transcriptional levels. We use biotagging to characterize the in vivo transcriptional landscape of migratory neural crest and myocardial cells in different cellular compartments (ribosomes and nucleus). These analyses reveal a comprehensive network of coding and non-coding RNAs and cis-regulatory modules, demonstrating that tissue-specific identity is embedded in the nuclear transcriptomes. By eliminating background inherent to complex embryonic environments, biotagging allows analyses of molecular interactions at high resolution. Biotagging enables cell- and compartment-specific in vivo biotinylation in zebrafish Technique yields comprehensive nuclear transcriptional analysis of cardiomyocytes Biotagging finds bidirectionally transcribed neural crest cis-regulatory modules System reveals tissue-specific regulation of noncoding RNA species
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Affiliation(s)
- Le A Trinh
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatiana Hochgreb-Hägele
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Upeka Senanayake
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Scott E Fraser
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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136
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Foley SW, Gosai SJ, Wang D, Selamoglu N, Sollitti AC, Köster T, Steffen A, Lyons E, Daldal F, Garcia BA, Staiger D, Deal RB, Gregory BD. A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate. Dev Cell 2017; 41:204-220.e5. [PMID: 28441533 PMCID: PMC5605909 DOI: 10.1016/j.devcel.2017.03.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/13/2017] [Accepted: 03/24/2017] [Indexed: 01/22/2023]
Abstract
The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. This analysis reveals distinct structural and protein binding patterns across both transcriptomes, allowing identification of differential RNA binding protein (RBP) recognition sites. Using these sequences, we identify two RBPs that regulate hair cell development. Specifically, we find that SERRATE functions in a microRNA-dependent manner to inhibit hair cell fate, while also terminating growth of root hairs mostly independent of microRNA biogenesis. In addition, we show that GLYCINE-RICH PROTEIN 8 promotes hair cell fate while alleviating phosphate starvation stress. In total, this global analysis reveals post-transcriptional regulators of plant root epidermal cell fate.
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Affiliation(s)
- Shawn W Foley
- Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sager J Gosai
- Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA
| | - Dongxue Wang
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Nur Selamoglu
- Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA
| | - Amelia C Sollitti
- Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA
| | - Tino Köster
- Department of Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld 33615, Germany
| | - Alexander Steffen
- Department of Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld 33615, Germany
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dorothee Staiger
- Department of Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld 33615, Germany
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
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137
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Qu X, Peterson KM, Torii KU. Stomatal development in time: the past and the future. Curr Opin Genet Dev 2017; 45:1-9. [PMID: 28219014 DOI: 10.1016/j.gde.2017.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 01/07/2023]
Abstract
Stomata have significantly diversified in nature since their first appearance around 400 million years ago. The diversification suggests the active reprogramming of molecular machineries of stomatal development during evolution. This review focuses on recent progress that sheds light on how this rewiring occurred in different organisms. Three specific aspects are discussed in this review: (i) the evolution of the transcriptional complex that governs stomatal state transitions; (ii) the evolution of receptor-ligand pairs that mediate extrinsic signaling; and (iii) the loss of stomatal development genes in an astomatous angiosperm.
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Affiliation(s)
- Xian Qu
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Kylee M Peterson
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-1800, USA; Institute of Transformative Biomolecules, Nagoya University, Nagoya, Aichi 464-8601, Japan.
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138
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Wang G, Köhler C. Epigenetic processes in flowering plant reproduction. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:797-807. [PMID: 28062591 DOI: 10.1093/jxb/erw486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Seeds provide up to 70% of the energy intake of the human population, emphasizing the relevance of understanding the genetic and epigenetic mechanisms controlling seed formation. In flowering plants, seeds are the product of a double fertilization event, leading to the formation of the embryo and the endosperm surrounded by maternal tissues. Analogous to mammals, plants undergo extensive epigenetic reprogramming during both gamete formation and early seed development, a process that is supposed to be required to enforce silencing of transposable elements and thus to maintain genome stability. Global changes of DNA methylation, histone modifications, and small RNAs are closely associated with epigenome programming during plant reproduction. Here, we review current knowledge on chromatin changes occurring during sporogenesis and gametogenesis, as well as early seed development in major flowering plant models.
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Affiliation(s)
- Guifeng Wang
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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139
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Zhou P, Gu F, Zhang L, Akerberg BN, Ma Q, Li K, He A, Lin Z, Stevens SM, Zhou B, Pu WT. Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq. eLife 2017; 6:22039. [PMID: 28121289 PMCID: PMC5295818 DOI: 10.7554/elife.22039] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
Understanding the mechanisms that regulate cell type-specific transcriptional programs requires developing a lexicon of their genomic regulatory elements. We developed a lineage-selective method to map transcriptional enhancers, regulatory genomic regions that activate transcription, in mice. Since most tissue-specific enhancers are bound by the transcriptional co-activator Ep300, we used Cre-directed, lineage-specific Ep300 biotinylation and pulldown on immobilized streptavidin followed by next generation sequencing of co-precipitated DNA to identify lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancers identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization. Our strategy for tissue-specific protein biotinylation opens new avenues for studying lineage-specific protein-DNA and protein-protein interactions.
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Affiliation(s)
- Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Fei Gu
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Lina Zhang
- Department of Biochemistry, Institute of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Kai Li
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Aibin He
- Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhiqiang Lin
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Sean M Stevens
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Bin Zhou
- State Key Laboratory of Cell Biology, CAS center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, United States
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140
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Moreno-Romero J, Santos-González J, Hennig L, Köhler C. Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles. Nat Protoc 2017; 12:238-254. [PMID: 28055034 DOI: 10.1038/nprot.2016.167] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The early endosperm tissue of dicot species is very difficult to isolate by manual dissection. This protocol details how to apply the INTACT (isolation of nuclei tagged in specific cell types) system for isolating early endosperm nuclei of Arabidopsis at high purity and how to generate parental-specific epigenome profiles. As a Protocol Extension, this article describes an adaptation of an existing Nature Protocol that details the use of the INTACT method for purification of root nuclei. We address how to obtain the INTACT lines, generate the starting material and purify the nuclei. We describe a method that allows purity assessment, which has not been previously addressed. The purified nuclei can be used for ChIP and DNA bisulfite treatment followed by next-generation sequencing (seq) to study histone modifications and DNA methylation profiles, respectively. By using two different Arabidopsis accessions as parents that differ by a large number of single-nucleotide polymorphisms (SNPs), we were able to distinguish the parental origin of epigenetic modifications. Our protocol describes the only working method to our knowledge for generating parental-specific epigenome profiles of the early Arabidopsis endosperm. The complete protocol, from silique collection to finished libraries, can be completed in 2 d for bisulfite-seq (BS-seq) and 3 to 4 d for ChIP-seq experiments.This protocol is an extension to: Nat. Protoc. 6, 56-68 (2011); doi:10.1038/nprot.2010.175; published online 16 December 2010.
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Affiliation(s)
- Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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141
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142
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Tekleyohans DG, Nakel T, Groß-Hardt R. Patterning the Female Gametophyte of Flowering Plants. PLANT PHYSIOLOGY 2017; 173:122-129. [PMID: 27920158 PMCID: PMC5210745 DOI: 10.1104/pp.16.01472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/02/2016] [Indexed: 05/07/2023]
Abstract
Intracellular and intercellular mechanisms govern the differentiation of female gametophytic cells.
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Affiliation(s)
| | - Thomas Nakel
- Molecular Genetics, Bremen University, 28359 Bremen, Germany
| | - Rita Groß-Hardt
- Molecular Genetics, Bremen University, 28359 Bremen, Germany
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143
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Vragović K, Bartom E, Savaldi-Goldstein S. Quantitation of Cell Type-Specific Responses to Brassinosteroid by Deep Sequencing of Polysome-Associated Polyadenylated RNA. Methods Mol Biol 2017; 1564:81-102. [PMID: 28124248 DOI: 10.1007/978-1-4939-6813-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hormonal signaling pathways control almost every aspect of plant physiology and development. Extensive analysis of hormonal signaling output, i.e., gene expression, has therefore been the focus of many studies. These analyses have been primarily conducted on total extracts derived from a mixture of tissues and cell types, consequentially limiting delineation of precise models. In this chapter, methods for tissue-specific functional genomics are overviewed, in which hormonal responses are analyzed at the transcriptional and the translational levels. Deep sequencing of polysome-associated polyadenylated RNA is employed for cell type-specific quantitation of translatome responses to brassinosteroids. Polysomes are purified by the previously established Translating Ribosome Affinity Purification (TRAP) method, in which the expression of a tagged ribosomal protein is targeted to the tissue of interest, allowing tissue-specific immunopurification of the polysome complexes. The methods presented assess establishment and selection of suitable transgenic lines. A protocol for hormonal treatment of the Arabidopsis thaliana root as a case study, TRAP and linear amplification of the purified polysome-associated polyadenylated RNA are described. Finally, a step-by-step presentation is included of the analysis of the RNA deep-sequencing data and Rscript for plotting hierarchically clustered heatmap of the expressed genes.
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Affiliation(s)
- Kristina Vragović
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Elizabeth Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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144
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Pindyurin AV. Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila. Methods Mol Biol 2017; 1654:99-124. [PMID: 28986785 DOI: 10.1007/978-1-4939-7231-9_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A thorough study of the genome-wide binding patterns of chromatin proteins is essential for understanding the regulatory mechanisms of genomic processes in eukaryotic nuclei, including DNA replication, transcription, and repair. The DNA adenine methyltransferase identification (DamID) method is a powerful tool to identify genomic binding sites of chromatin proteins. This method does not require fixation of cells and the use of specific antibodies, and has been used to generate genome-wide binding maps of more than a hundred different proteins in Drosophila tissue culture cells. Recent versions of inducible DamID allow performing cell type-specific profiling of chromatin proteins even in small samples of Drosophila tissues that contain heterogeneous cell types. Importantly, with these methods sorting of cells of interest or their nuclei is not necessary as genomic DNA isolated from the whole tissue can be used as an input. Here, I describe in detail an FLP-inducible DamID method, namely generation of suitable transgenic flies, activation of the Dam transgenes by the FLP recombinase, isolation of DNA from small amounts of dissected tissues, and subsequent identification of the DNA binding sites of the chromatin proteins.
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Affiliation(s)
- Alexey V Pindyurin
- Laboratory of Cell Division, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia.
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145
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Wang H, Lan P, Shen RF. Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs. Proteomics 2016; 16:877-93. [PMID: 26749523 DOI: 10.1002/pmic.201500265] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 12/28/2015] [Accepted: 01/05/2016] [Indexed: 11/11/2022]
Abstract
Plants and other multicellular organisms consist of many types of specialized cells. Systems-wide exploration of large-scale information from singe cell level is essential to understand how cell works. Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, in the interaction with microbe, and in plant anchorage, and represent an ideal model to study the biology of a single cell type. Single cell sampling combined with omics approaches has been applied to study plant root hairs. This review emphasizes the integration of omics approaches towards understanding the systems biology of root hairs, unraveling the common and plant species-specific properties of root hairs, as well as the concordance of protein and transcript abundance. Understanding plant root hair biology by mining the integrated omics data will provide a way to know how a single cell differentiates, elongates, and functions, which might help molecularly modify crops for developing sustainable agriculture practices.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, P. R. China
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146
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Ye Y, Li M, Gu L, Chen X, Shi J, Zhang X, Jiang C. Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. Cell Death Differ 2016; 24:409-420. [PMID: 27858939 PMCID: PMC5344203 DOI: 10.1038/cdd.2016.135] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 12/25/2022] Open
Abstract
Neurons are a key component of the nervous system and differentiate from multipotent neural stem cells (NSCs). Chromatin remodeling has a critical role in the differentiation process. However, its in vivo epigenetic regulatory role remains unknown. We show here that nucleosome depletion regions (NDRs) form in both proximal promoters and distal enhancers during NSCs differentiating into neurons in the early Drosophila embryonic development. NDR formation in the regulatory regions involves nucleosome shift and eviction. Nucleosome occupancy in promoter NDRs is inversely proportional to the gene activity. Genes with promoter NDR formation during differentiation are enriched for functions related to neuron development and maturation. Active histone-modification signals (H3K4me3 and H3K9ac) in promoters are gained in neurons in two modes: de novo establishment to high levels or increase from the existing levels in NSCs. The gene sets corresponding to the two modes have different neuron-related functions. Dynamic changes of H3K27ac and H3K9ac signals in enhancers and promoters synergistically repress genes associated with neural stem or progenitor cell-related pluripotency and upregulate genes associated with neuron projection morphogenesis, neuron differentiation, and so on. Our results offer new insights into chromatin remodeling during in vivo neuron development and lay a foundation for its epigenetic regulatory mechanism study of other lineage specification.
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Affiliation(s)
- Youqiong Ye
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Min Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Xiaolong Chen
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Jiejun Shi
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Xiaobai Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
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147
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Hirano Y, Ihara K, Masuda T, Yamamoto T, Iwata I, Takahashi A, Awata H, Nakamura N, Takakura M, Suzuki Y, Horiuchi J, Okuno H, Saitoe M. Shifting transcriptional machinery is required for long-term memory maintenance and modification in Drosophila mushroom bodies. Nat Commun 2016; 7:13471. [PMID: 27841260 PMCID: PMC5114576 DOI: 10.1038/ncomms13471] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 10/06/2016] [Indexed: 01/08/2023] Open
Abstract
Accumulating evidence suggests that transcriptional regulation is required for maintenance of long-term memories (LTMs). Here we characterize global transcriptional and epigenetic changes that occur during LTM storage in the Drosophila mushroom bodies (MBs), structures important for memory. Although LTM formation requires the CREB transcription factor and its coactivator, CBP, subsequent early maintenance requires CREB and a different coactivator, CRTC. Late maintenance becomes CREB independent and instead requires the transcription factor Bx. Bx expression initially depends on CREB/CRTC activity, but later becomes CREB/CRTC independent. The timing of the CREB/CRTC early maintenance phase correlates with the time window for LTM extinction and we identify different subsets of CREB/CRTC target genes that are required for memory maintenance and extinction. Furthermore, we find that prolonging CREB/CRTC-dependent transcription extends the time window for LTM extinction. Our results demonstrate the dynamic nature of stored memory and its regulation by shifting transcription systems in the MBs. Transcriptional regulation is necessary for maintaining long-term memories (LTM) but the mechanistic details are not completely defined. Here the authors identify transcriptional machinery and histone modifiers required for LTM maintenance in Drosophila and show that transcriptional regulation for LTM maintenance is distinct from that for LTM formation.
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Affiliation(s)
- Yukinori Hirano
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.,Japan Science and Technology Agency, PRESTO, 4-4-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kunio Ihara
- Center of Gene Research, Nagoya University, Huro-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomoko Masuda
- Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-0057, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Department of Reprogramming Science, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan.,AMED-CREST, AMED 1-7-1 Otemach, Chiyodaku, Tokyo 100-0004, Japan
| | - Ikuko Iwata
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Aya Takahashi
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroko Awata
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naosuke Nakamura
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.,Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto City 603-8555, Japan
| | - Mai Takakura
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yusuke Suzuki
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Junjiro Horiuchi
- Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-0057, Japan
| | - Hiroyuki Okuno
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Minoru Saitoe
- Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-0057, Japan
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148
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Shirakawa M, Ueda H, Shimada T, Hara-Nishimura I. FAMA: A Molecular Link between Stomata and Myrosin Cells. TRENDS IN PLANT SCIENCE 2016; 21:861-871. [PMID: 27477926 DOI: 10.1016/j.tplants.2016.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/24/2016] [Accepted: 07/04/2016] [Indexed: 05/04/2023]
Abstract
Plants use sophisticated defense strategies against herbivores, including the myrosinase-glucosinolate system in Brassicales plants. This system sequesters myrosinase in myrosin cells, which are idioblasts in inner leaf tissues, and produces a toxic compound when cells are damaged by herbivores. Although the molecular mechanisms underlying myrosin cell development are largely unknown, recent studies have revealed that two key components, a basic helix-loop-helix (bHLH) transcription factor (FAMA) and vesicle trafficking factors (such as SYNTAXIN OF PLANTS 22), regulate the differentiation and fate determination of myrosin cells. FAMA also functions as a master regulator of guard cell (GC) differentiation. In this review, we discuss how FAMA operates two distinct genetic programs: the generation of myrosin cells in inner plant tissue and GCs in the epidermis.
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Affiliation(s)
- Makoto Shirakawa
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Haruko Ueda
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Tomoo Shimada
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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149
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Park K, Frost JM, Adair AJ, Kim DM, Yun H, Brooks JS, Fischer RL, Choi Y. Optimized Methods for the Isolation of Arabidopsis Female Central Cells and Their Nuclei. Mol Cells 2016; 39:768-775. [PMID: 27788573 PMCID: PMC5104886 DOI: 10.14348/molcells.2016.0209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022] Open
Abstract
The Arabidopsis female gametophyte contains seven cells with eight haploid nuclei buried within layers of sporophytic tissue. Following double fertilization, the egg and central cells of the gametophyte develop into the embryo and endosperm of the seed, respectively. The epigenetic status of the central cell has long presented an enigma due both to its inaccessibility, and the fascinating epigenome of the endosperm, thought to have been inherited from the central cell following activity of the DEMETER demethylase enzyme, prior to fertilization. Here, we present for the first time, a method to isolate pure populations of Arabidopsis central cell nuclei. Utilizing a protocol designed to isolate leaf mesophyll protoplasts, we systematically optimized each step in order to efficiently separate central cells from the female gametophyte. We use initial manual pistil dissection followed by the derivation of central cell protoplasts, during which process the central cell emerges from the micropylar pole of the embryo sac. Then, we use a modified version of the Isolation of Nuclei TAgged in specific Cell Types (INTACT) protocol to purify central cell nuclei, resulting in a purity of 75-90% and a yield sufficient to undertake downstream molecular analyses. We find that the process is highly dependent on the health of the original plant tissue used, and the efficiency of protoplasting solution infiltration into the gametophyte. By isolating pure central cell populations, we have enabled elucidation of the physiology of this rare cell type, which in the future will provide novel insights into Arabidopsis reproduction.
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Affiliation(s)
- Kyunghyuk Park
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
| | - Jennifer M. Frost
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720,
USA
| | - Adam James Adair
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720,
USA
| | - Dong Min Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
| | - Hyein Yun
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
| | - Janie S. Brooks
- Department of Science, Seoul Foreign School, Seoul 09723,
Korea
| | - Robert L. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720,
USA
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
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150
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de Lucas M, Pu L, Turco G, Gaudinier A, Morao AK, Harashima H, Kim D, Ron M, Sugimoto K, Roudier F, Brady SM. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation. THE PLANT CELL 2016; 28:2616-2631. [PMID: 27650334 PMCID: PMC5134969 DOI: 10.1105/tpc.15.00744] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 08/29/2016] [Accepted: 09/14/2016] [Indexed: 05/21/2023]
Abstract
Spatiotemporal regulation of transcription is fine-tuned at multiple levels, including chromatin compaction. Polycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of Histone 3 at lysine 27 (H3K27me3), which is the hallmark of a repressive chromatin state. Multiple PRC2 complexes have been reported in Arabidopsis thaliana to control the expression of genes involved in developmental transitions and maintenance of organ identity. Here, we show that PRC2 member genes display complex spatiotemporal gene expression patterns and function in root meristem and vascular cell proliferation and specification. Furthermore, PRC2 gene expression patterns correspond with vascular and nonvascular tissue-specific H3K27me3-marked genes. This tissue-specific repression via H3K27me3 regulates the balance between cell proliferation and differentiation. Using enhanced yeast one-hybrid analysis, upstream regulators of the PRC2 member genes are identified, and genetic analysis demonstrates that transcriptional regulation of some PRC2 genes plays an important role in determining PRC2 spatiotemporal activity within a developing organ.
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Affiliation(s)
- Miguel de Lucas
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Li Pu
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Gina Turco
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Dahae Kim
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mily Ron
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Francois Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
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