1
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Gouran M, Brady SM. The transcriptional integration of environmental cues with root cell type development. PLANT PHYSIOLOGY 2024:kiae425. [PMID: 39288006 DOI: 10.1093/plphys/kiae425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/05/2024] [Indexed: 09/19/2024]
Abstract
Plant roots navigate the soil ecosystem with each cell type uniquely responding to environmental stimuli. Below ground, the plant's response to its surroundings is orchestrated at the cellular level, including morphological and molecular adaptations that shape root system architecture as well as tissue and organ functionality. Our understanding of the transcriptional responses at cell type resolution has been profoundly enhanced by studies of the model plant Arabidopsis thaliana. However, both a comprehensive view of the transcriptional basis of these cellular responses to single and combinatorial environmental cues in diverse plant species remains elusive. In this review, we highlight the ability of root cell types to undergo specific anatomical or morphological changes in response to abiotic and biotic stresses or cues and how they collectively contribute to the plant's overall physiology. We further explore interconnections between stress and the temporal nature of developmental pathways and discuss examples of how this transcriptional reprogramming influences cell type identity and function. Finally, we highlight the power of single-cell and spatial transcriptomic approaches to refine our understanding of how environmental factors fine tune root spatiotemporal development. These complex root system responses underscore the importance of spatiotemporal transcriptional mapping, with significant implications for enhanced agricultural resilience.
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Affiliation(s)
- Mona Gouran
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
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2
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Takagi H, Ito S, Shim JS, Kubota A, Hempton AK, Lee N, Suzuki T, Yang C, Nolan CT, Bubb KL, Alexandre CM, Kurihara D, Sato Y, Tada Y, Kiba T, Pruneda-Paz JL, Queitsch C, Cuperus JT, Imaizumi T. A florigen-expressing subpopulation of companion cells expresses other small proteins and reveals a nitrogen-sensitive FT repressor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.17.608367. [PMID: 39229231 PMCID: PMC11370445 DOI: 10.1101/2024.08.17.608367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T (FT) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes, FT is induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of the FT-expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression in FT-expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated that FT-expressing cells in cotyledons and in true leaves differed transcriptionally. Within the true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogous NIGT1.2 and NIGT1.4 repressed FT expression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that major FT-expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development.
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Affiliation(s)
- Hiroshi Takagi
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Shogo Ito
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Jae Sung Shim
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, South Korea
| | - Akane Kubota
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
- Division of Biological Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Andrew K Hempton
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Nayoung Lee
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
- Research Institute of Molecular Alchemy (RIMA), Gyeongsang National University, Jinju, 52828, South Korea
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501, Japan
| | - Chansie Yang
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Christine T Nolan
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Cristina M Alexandre
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Daisuke Kurihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
- Institute for Advanced Research (IAR), Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Takatoshi Kiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Jose L Pruneda-Paz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
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3
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Martin RA, Viggars MR, Sanford JA, Taylor ZW, Hansen JR, Clair GC, Adkins JN, Douglas CM, Esser KA. Alterations of the skeletal muscle nuclear proteome after acute exercise reveals a post-transcriptional influence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607176. [PMID: 39149399 PMCID: PMC11326304 DOI: 10.1101/2024.08.08.607176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Exercise is firmly established as a key contributor to overall well-being and is frequently employed as a therapeutic approach to mitigate various health conditions. One pivotal aspect of the impact of exercise lies in the systemic transcriptional response, which underpins its beneficial adaptations. While extensive research has been devoted to understanding the transcriptional response to exercise, our knowledge of the protein constituents of nuclear processes that accompany gene expression in skeletal muscle remains largely elusive. We hypothesize that alterations in the nuclear proteome following exercise hold vital clues for comprehending the transcriptional regulation and other related nuclear functions. We isolated skeletal muscle nuclei from C57BL/6 mice both sedentary control and one-hour post 30-minute treadmill running, to gain insights into the nuclear proteome after exercise. A substantial number of the 2,323 proteins identified, were related to nuclear functions. For instance, we found 59 proteins linked to nucleocytoplasmic transport were higher in sedentary mice compared to exercise, hinting at an exercise-induced modulation to nuclear trafficking. Furthermore, 135 proteins exhibited increased abundance after exercise (FDR < 0.1) while 89 proteins decreased, with the most prominent changes in proteins linked to mRNA processing and splicing. Super resolution microscopy further highlights potential localization change in mRNA processing proteins post-exercise, further suggesting changes in nuclear transport dynamics. Nonetheless, our data provide important considerations for the study of the nuclear proteome and supports a paradigm through which exercise downregulated mRNA processing and splicing, offering valuable insights into the broader landscape of the impact from acute exercise. New & Noteworthy Exercise plays a crucial role in promoting muscle health, but our understanding of nuclear proteins orchestrating exercise responses is limited. Isolation of skeletal muscle nuclei coupled with mass spectrometry enhanced the identification of nuclear proteins. This approach was used to investigate the effects of acute exercise, revealing changes in the muscle nuclear proteome 1-hour post-exercise, including proteins linked to post-transcriptional processing and splicing. Our findings offer insights into the exercise-induced changes within muscle nuclear proteins.
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Affiliation(s)
- Ryan A. Martin
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | - Mark R. Viggars
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | | | - Zane W. Taylor
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Joshua N. Adkins
- Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Collin M. Douglas
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
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4
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Plskova Z, Van Breusegem F, Kerchev P. Redox regulation of chromatin remodelling in plants. PLANT, CELL & ENVIRONMENT 2024; 47:2780-2792. [PMID: 38311877 DOI: 10.1111/pce.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024]
Abstract
Changes in the cellular redox balance that occur during plant responses to unfavourable environmental conditions significantly affect a myriad of redox-sensitive processes, including those that impact on the epigenetic state of the chromatin. Various epigenetic factors, like histone modifying enzymes, chromatin remodelers, and DNA methyltransferases can be targeted by oxidative posttranslational modifications. As their combined action affects the epigenetic regulation of gene expression, they form an integral part of plant responses to (a)biotic stress. Epigenetic changes triggered by unfavourable environmental conditions are intrinsically linked with primary metabolism that supplies intermediates and donors, such acetyl-CoA and S-adenosyl-methionine, that are critical for the epigenetic decoration of histones and DNA. Here, we review the recent advances in our understanding of redox regulation of chromatin remodelling, dynamics of epigenetic marks, and the interplay between epigenetic control of gene expression, redox signalling and primary metabolism within an (a)biotic stress context.
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Affiliation(s)
- Zuzana Plskova
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Frank Van Breusegem
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, UGent, Ghent, Belgium
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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5
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Chucair-Elliott AJ, Ocañas SR, Pham K, Machalinski A, Plafker S, Stout MB, Elliott MH, Freeman WM. Age- and sex- divergent translatomic responses of the mouse retinal pigmented epithelium. Neurobiol Aging 2024; 140:41-59. [PMID: 38723422 PMCID: PMC11173338 DOI: 10.1016/j.neurobiolaging.2024.04.012] [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] [Received: 10/24/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Aging is the main risk factor for age-related macular degeneration (AMD), a retinal neurodegenerative disease that leads to irreversible blindness, particularly in people over 60 years old. Retinal pigmented epithelium (RPE) atrophy is an AMD hallmark. Genome-wide chromatin accessibility, DNA methylation, and gene expression studies of AMD and control RPE demonstrate epigenomic/transcriptomic changes occur during AMD onset and progression. However, mechanisms by which molecular alterations of normal aging impair RPE function and contribute to AMD pathogenesis are unclear. Here, we specifically interrogate the RPE translatome with advanced age and across sexes in a novel RPE reporter mouse model. We find differential age- and sex- associated transcript expression with overrepresentation of pathways related to inflammation in the RPE. Concordant with impaired RPE function, the phenotypic changes in the aged translatome suggest that aged RPE becomes immunologically active, in both males and females, with some sex-specific signatures, which supports the need for sex representation for in vivo studies.
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Affiliation(s)
- Ana J Chucair-Elliott
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
| | - Sarah R Ocañas
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Adeline Machalinski
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Scott Plafker
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael B Stout
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael H Elliott
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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6
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Fu J, McKinley B, James B, Chrisler W, Markillie LM, Gaffrey MJ, Mitchell HD, Riaz MR, Marcial B, Orr G, Swaminathan K, Mullet J, Marshall-Colon A. Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1668-1688. [PMID: 38407828 DOI: 10.1111/tpj.16690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/17/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/).
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Affiliation(s)
- Jie Fu
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Brandon James
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - William Chrisler
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | | | - Matthew J Gaffrey
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Hugh D Mitchell
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Muhammad Rizwan Riaz
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Brenda Marcial
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - Galya Orr
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Kankshita Swaminathan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
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7
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Romani F, Sauret-Güeto S, Rebmann M, Annese D, Bonter I, Tomaselli M, Dierschke T, Delmans M, Frangedakis E, Silvestri L, Rever J, Bowman JL, Romani I, Haseloff J. The landscape of transcription factor promoter activity during vegetative development in Marchantia. THE PLANT CELL 2024; 36:2140-2159. [PMID: 38391349 PMCID: PMC11132968 DOI: 10.1093/plcell/koae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/08/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024]
Abstract
Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.
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Affiliation(s)
- Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Marius Rebmann
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Davide Annese
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Ignacy Bonter
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Linda Silvestri
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Ignacio Romani
- Departamento de Ciencias Sociales, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
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8
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Hsieh JWA, Lin PY, Wang CT, Lee YJ, Chang P, Lu RJH, Chen PY, Wang CJR. Establishing an optimized ATAC-seq protocol for the maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1370618. [PMID: 38863553 PMCID: PMC11165127 DOI: 10.3389/fpls.2024.1370618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin structure is found to collaborate with massive transcriptional variations across tissues and developmental stages, implying intricate regulatory mechanisms, which highlights the importance of integrating chromatin information into breeding strategies for precise gene controls. The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. In this context, we developed an easy-to-implement ATAC-seq protocol for maize with fewer nuclei and simple equipment. We demonstrate a streamlined ATAC-seq protocol with four key steps for maize in which nuclei purification can be achieved without cell sorting and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, including validation by read length periodicity, key metrics, and correlation with transcript abundance, provides a precise and efficient assessment of the maize chromatin landscape. Beyond its application to maize, our testing design holds the potential to be applied to other crops or other tissues, especially for those with limited size and amount, establishing a robust foundation for chromatin structure studies in diverse crop species.
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Affiliation(s)
- Jo-Wei Allison Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Jing Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Tropical Agriculture and International Cooperation/Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Rita Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
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9
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Simon L, Probst AV. Maintenance and dynamic reprogramming of chromatin organization during development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:657-670. [PMID: 36700345 DOI: 10.1111/tpj.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Abstract
Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.
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Affiliation(s)
- Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
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10
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Luna-García V, Bernal Gallardo JJ, Rethoret-Pasty M, Pasha A, Provart NJ, de Folter S. A high-resolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis. PLANT PHYSIOLOGY 2024; 195:410-429. [PMID: 38088205 DOI: 10.1093/plphys/kiad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/14/2023] [Indexed: 05/02/2024]
Abstract
Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive competence of angiosperms. In Arabidopsis (Arabidopsis thaliana), the gynoecium is composed of two fused carpels with different tissues that need to develop and differentiate to form a mature gynoecium and thus the reproductive competence of Arabidopsis. For these reasons, they have become the object of study for floral and fruit development. However, due to the complexity of the gynoecium, specific spatio-temporal tissue expression patterns are still scarce. In this study, we used precise laser-assisted microdissection and high-throughput RNA sequencing to describe the transcriptional profiles of the medial and lateral domain tissues of the Arabidopsis gynoecium. We provide evidence that the method used is reliable and that, in addition to corroborating gene expression patterns of previously reported regulators of these tissues, we found genes whose expression dynamics point to being involved in cytokinin and auxin homeostasis and in cell cycle progression. Furthermore, based on differential gene expression analyses, we functionally characterized several genes and found that they are involved in gynoecium development. This resource is available via the Arabidopsis eFP browser and will serve the community in future studies on developmental and reproductive biology.
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Affiliation(s)
- Valentín Luna-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Judith Jazmin Bernal Gallardo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Martin Rethoret-Pasty
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
- Polytech Nice Sophia, Université Côte d'Azur, 930 Rte des Colles, 06410 Biot, France
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
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11
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Takagi H, Lee N, Hempton AK, Purushwani S, Notaguchi M, Yamauchi K, Shirai K, Kawakatsu Y, Uehara S, Albers WG, Downing BLR, Ito S, Suzuki T, Matsuura T, Mori IC, Mitsuda N, Kurihara D, Matsushita T, Song YH, Sato Y, Nomoto M, Tada Y, Hanada K, Cuperus JT, Queitsch C, Imaizumi T. Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591289. [PMID: 38746097 PMCID: PMC11092471 DOI: 10.1101/2024.04.26.591289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Seasonal changes in spring induce flowering by expressing the florigen, FLOWERING LOCUS T (FT), in Arabidopsis. FT is expressed in unique phloem companion cells with unknown characteristics. The question of which genes are co-expressed with FT and whether they have roles in flowering remains elusive. Through tissue-specific translatome analysis, we discovered that under long-day conditions with the natural sunlight red/far-red ratio, the FT-producing cells express a gene encoding FPF1-LIKE PROTEIN 1 (FLP1). The master FT regulator, CONSTANS (CO), controls FLP1 expression, suggesting FLP1's involvement in the photoperiod pathway. FLP1 promotes early flowering independently of FT, is active in the shoot apical meristem, and induces the expression of SEPALLATA 3 (SEP3), a key E-class homeotic gene. Unlike FT, FLP1 facilitates inflorescence stem elongation. Our cumulative evidence indicates that FLP1 may act as a mobile signal. Thus, FLP1 orchestrates floral initiation together with FT and promotes inflorescence stem elongation during reproductive transitions.
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Affiliation(s)
- Hiroshi Takagi
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Nayoung Lee
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Andrew K. Hempton
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
| | - Savita Purushwani
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Kota Yamauchi
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Kazumasa Shirai
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Yaichi Kawakatsu
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan
| | - Susumu Uehara
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - William G. Albers
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
| | | | - Shogo Ito
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Izumi C. Mori
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Daisuke Kurihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
- Institute for Advanced Research (IAR), Nagoya University, Nagoya, 464-8601, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Young Hun Song
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Josh T. Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195-5065, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195-5065, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, 98195-8047, USA
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington, 98195-1800, USA
- Center for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
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12
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Santhanagopalan I, Netzl A, Mathur T, Smith A, Griffiths H, Holzer A. Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing. STAR Protoc 2024; 5:102764. [PMID: 38236771 PMCID: PMC10828896 DOI: 10.1016/j.xpro.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/13/2023] [Accepted: 11/21/2023] [Indexed: 02/03/2024] Open
Abstract
The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.
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Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
| | - Antonia Netzl
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Tanya Mathur
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alison Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Center for Bioinformatics and Department of Computer Science, Saarland University, 66123 Saarbrücken, Germany.
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13
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Yaschenko AE, Alonso JM, Stepanova AN. Arabidopsis as a model for translational research. THE PLANT CELL 2024:koae065. [PMID: 38411602 DOI: 10.1093/plcell/koae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.
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Affiliation(s)
- Anna E Yaschenko
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
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14
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Lu C, Wei Y, Abbas M, Agula H, Wang E, Meng Z, Zhang R. Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects. Int J Mol Sci 2024; 25:1479. [PMID: 38338756 PMCID: PMC10855595 DOI: 10.3390/ijms25031479] [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] [Received: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be inferred at single-cell resolution. This cutting-edge technology now enables the genome-wide profiling of chromatin accessibility at the cellular level and the capturing of cell-type-specific cis-regulatory elements (CREs) that are masked by cellular heterogeneity in bulk assays. Additionally, it can also facilitate the identification of rare and new cell types based on differences in chromatin accessibility and the charting of cellular developmental trajectories within lineage-related cell clusters. Due to technical challenges and limitations, the data generated from scATAC-seq exhibit unique features, often characterized by high sparsity and noise, even within the same cell type. To address these challenges, various bioinformatic tools have been developed. Furthermore, the application of scATAC-seq in plant science is still in its infancy, with most research focusing on root tissues and model plant species. In this review, we provide an overview of recent progress in scATAC-seq and its application across various fields. We first conduct scATAC-seq in plant science. Next, we highlight the current challenges of scATAC-seq in plant science and major strategies for cell type annotation. Finally, we outline several future directions to exploit scATAC-seq technologies to address critical challenges in plant science, ranging from plant ENCODE(The Encyclopedia of DNA Elements) project construction to GRN inference, to deepen our understanding of the roles of CREs in plant biology.
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Affiliation(s)
- Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Hasi Agula
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
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15
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Raskina O, Hakim O. Rapid DNA-FISH in Arabidopsis thaliana Somatic Cells. Methods Mol Biol 2024; 2784:259-270. [PMID: 38502491 DOI: 10.1007/978-1-0716-3766-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Fluorescence in situ hybridization (FISH) technique has been widely used to detect and localize specific DNA and RNA sequences in interphase nuclei and chromosomes in animals and plants. Here, we present a protocol for localization of genomic loci in nuclei of the model plant Arabidopsis thaliana. This protocol includes several advances and adaptations to A. thaliana, including preparation of nuclei and chromosomes without the use of liquid nitrogen, and an in situ hybridization procedure that preserves chromatin structure without the use of paraformaldehyde and formamide. Simultaneous denaturation of the BAC (bacterial artificial chromosome) probe and nuclei followed by annealing at high temperature allows hybridization in less than an hour. These hybridization conditions also provide high signal to noise ratio by a small number of washes. Thus, this simplified in situ hybridization procedure is completed in one working day.
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Affiliation(s)
- Olga Raskina
- Institute of Evolution, University of Haifa, Haifa, Israel.
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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16
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Manosalva Pérez N, Ferrari C, Engelhorn J, Depuydt T, Nelissen H, Hartwig T, Vandepoele K. MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:280-301. [PMID: 37788349 DOI: 10.1111/tpj.16483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/13/2023] [Accepted: 09/16/2023] [Indexed: 10/05/2023]
Abstract
Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.
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Affiliation(s)
- Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Camilla Ferrari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Julia Engelhorn
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Thomas Hartwig
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
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17
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Kellogg CM, Pham K, Ko S, Cox JE, Machalinski AH, Stout MB, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Specificity and efficiency of tamoxifen-mediated Cre induction is equivalent regardless of age. iScience 2023; 26:108413. [PMID: 38058312 PMCID: PMC10696116 DOI: 10.1016/j.isci.2023.108413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/15/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Temporally controlling Cre recombination through tamoxifen (Tam) induction has many advantages for biomedical research. Most studies report early post-natal/juvenile (<2 m.o.) Tam induction, but age-related neurodegeneration and aging studies can require Cre induction in older mice (>12 m.o.). While anecdotally reported as problematic, there are no published comparisons of Tam-mediated Cre induction at early and late ages. Here, microglial-specific Cx3cr1creERT2 mice were crossed to a floxed NuTRAP reporter to compare Cre induction at early (3-6 m.o.) and late (20 m.o.) ages. Specificity and efficiency of microglial labeling at 21-22 m.o. were identical in mice induced with Tam at early and late ages. Age-related microglial translatomic changes were also similar regardless of Tam induction age. Each Cre and flox mouse line should be independently validated, however, these findings demonstrate that Tam-mediated Cre induction can be performed even into older mouse ages and should be generalizable to other inducible Cre models.
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Affiliation(s)
- Collyn M. Kellogg
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sunghwan Ko
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jillian E.J. Cox
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael B. Stout
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Amanda L. Sharpe
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael J. Beckstead
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sarah R. Ocañas
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M. Freeman
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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18
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Pelayo MA, Yamaguchi N. Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor-chromatin dynamics. FRONTIERS IN PLANT SCIENCE 2023; 14:1323507. [PMID: 38155851 PMCID: PMC10753784 DOI: 10.3389/fpls.2023.1323507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023]
Abstract
The intricate morphology of the flower is primarily established within floral meristems in which floral organs will be defined and from where the developing flower will emerge. Floral meristem development involves multiscale-level regulation, including lineage and positional mechanisms for establishing cell-type identity, and transcriptional regulation mediated by changes in the chromatin environment. However, many key aspects of floral meristem development remain to be determined, such as: 1) the exact role of cellular location in connecting transcriptional inputs to morphological outcomes, and 2) the precise interactions between transcription factors and chromatin regulators underlying the transcriptional networks that regulate the transition from cell proliferation to differentiation during floral meristem development. Here, we highlight recent studies addressing these points through newly developed spatial reconstruction techniques and high-resolution transcription factor-chromatin environment interactions in the model plant Arabidopsis thaliana. Specifically, we feature studies that reconstructed 3D gene expression atlases of the floral meristem. We also discuss how the precise timing of floral meristem specification, floral organ patterning, and floral meristem termination is determined through temporally defined epigenetic dynamics for fine-tuning of gene expression. These studies offer fresh insights into the well-established principles of floral meristem development and outline the potential for further advances in this field in an age of integrated, powerful, multiscale resolution approaches.
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Affiliation(s)
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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19
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Skalický V, Antoniadi I, Pěnčík A, Chamrád I, Lenobel R, Kubeš MF, Zatloukal M, Žukauskaitė A, Strnad M, Ljung K, Novák O. Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1825-1841. [PMID: 37682018 DOI: 10.1111/tpj.16456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023]
Abstract
Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.
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Affiliation(s)
- Vladimír Skalický
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Martin F Kubeš
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Marek Zatloukal
- Department of Chemical Biology, Faculty of Science, Palacký University, CZ-78371, Olomouc, Czech Republic
| | - Asta Žukauskaitė
- Department of Chemical Biology, Faculty of Science, Palacký University, CZ-78371, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
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20
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 2023; 16:45. [PMID: 37953264 PMCID: PMC10642035 DOI: 10.1186/s13072-023-00522-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia. RESULTS After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. CONCLUSIONS Neurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.
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Affiliation(s)
- Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adeline H Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Walker Hoolehan
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adam M Kulpa
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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21
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You Y, Jiang Z. The eINTACT method for studying nuclear changes in host plant cells targeted by bacterial effectors in native infection contexts. Nat Protoc 2023; 18:3173-3193. [PMID: 37697105 DOI: 10.1038/s41596-023-00879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/23/2023] [Indexed: 09/13/2023]
Abstract
Type-III effector proteins are major virulence determinants that most gram-negative bacteria inject into host cells to manipulate cellular processes for infection. Because effector-targeted cells are embedded and underrepresented in infected plant tissues, it is technically challenging to isolate them for focused studies of effector-induced cellular changes. This protocol describes a novel technique, effector-inducible isolation of nuclei tagged in specific cell types (eINTACT), for isolating biotin-labeled nuclei from Arabidopsis plant cells that have received Xanthomonas bacterial effectors by using streptavidin-coated magnetic beads. This protocol is an extension of the existing Nature Protocols Protocol of the INTACT method for the affinity-based purification of nuclei of specific cell types in the context of developmental biology. In a phytopathology scenario, our protocol addresses how to obtain eINTACT transgenic lines and compatible bacterial mutants, verify the eINTACT system and purify nuclei of bacterial effector-recipient cells from infected tissues. Differential analyses of purified nuclei from plants infected by bacteria expressing the effector of interest and those from plants infected by effector-deletion bacterial mutants will reveal the effector-dependent nuclear changes in targeted host cells. Provided that the eINTACT system is available, the infection experiment takes 5 d, and the procedures, from collecting bacteria-infected leaves to obtaining nuclei of effector-targeted cells, can be completed in 4 h. eINTACT is a unique method for isolating high-quality nuclei from bacterial effector-targeted host cells in native infection contexts. This method is adaptable to study the functions of type-III effectors from numerous gram-negative bacteria in host plants that are amenable to transformation.
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Affiliation(s)
- Yuan You
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
- Department of General Genetics, Center for Plant Molecular Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany.
| | - Zhihao Jiang
- Department of Plant Biochemistry, Center for Plant Molecular Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany
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22
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Gruber T, Lechner F, Murat C, Contreras RE, Sanchez-Quant E, Miok V, Makris K, Le Thuc O, González-García I, García-Clave E, Althammer F, Krabichler Q, DeCamp LM, Jones RG, Lutter D, Williams RH, Pfluger PT, Müller TD, Woods SC, Pospisilik JA, Martinez-Jimenez CP, Tschöp MH, Grinevich V, García-Cáceres C. High-calorie diets uncouple hypothalamic oxytocin neurons from a gut-to-brain satiation pathway via κ-opioid signaling. Cell Rep 2023; 42:113305. [PMID: 37864798 PMCID: PMC10636643 DOI: 10.1016/j.celrep.2023.113305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/21/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023] Open
Abstract
Oxytocin-expressing paraventricular hypothalamic neurons (PVNOT neurons) integrate afferent signals from the gut, including cholecystokinin (CCK), to adjust whole-body energy homeostasis. However, the molecular underpinnings by which PVNOT neurons orchestrate gut-to-brain feeding control remain unclear. Here, we show that mice undergoing selective ablation of PVNOT neurons fail to reduce food intake in response to CCK and develop hyperphagic obesity on a chow diet. Notably, exposing wild-type mice to a high-fat/high-sugar (HFHS) diet recapitulates this insensitivity toward CCK, which is linked to diet-induced transcriptional and electrophysiological aberrations specifically in PVNOT neurons. Restoring OT pathways in diet-induced obese (DIO) mice via chemogenetics or polypharmacology sufficiently re-establishes CCK's anorexigenic effects. Last, by single-cell profiling, we identify a specialized PVNOT neuronal subpopulation with increased κ-opioid signaling under an HFHS diet, which restrains their CCK-evoked activation. In sum, we document a (patho)mechanism by which PVNOT signaling uncouples a gut-brain satiation pathway under obesogenic conditions.
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Affiliation(s)
- Tim Gruber
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49506, USA.
| | - Franziska Lechner
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Cahuê Murat
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Raian E Contreras
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Eva Sanchez-Quant
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
| | - Viktorian Miok
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Konstantinos Makris
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ophélia Le Thuc
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Ismael González-García
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Elena García-Clave
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | | | - Quirin Krabichler
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Lisa M DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA
| | - Dominik Lutter
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Rhiannan H Williams
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute for Neurogenomics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Paul T Pfluger
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit NeuroBiology of Diabetes, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Neurobiology of Diabetes, TUM School of Medicine, Technical University Munich, 80333 Munich, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Department of Pharmacology and Experimental Therapy, Institute for Experimental and Clinical Pharmacology and Toxicology, Eberhard Karls Hospitals and Clinics, Tübingen, Germany
| | - Stephen C Woods
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - John Andrew Pospisilik
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49506, USA; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49506, USA
| | - Celia P Martinez-Jimenez
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49506, USA; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität, Munich, Germany
| | - Valery Grinevich
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; Center for Neuroinflammation and Cardiometabolic Diseases, Georgia State University, Atlanta, GA, USA.
| | - Cristina García-Cáceres
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, 80336 Munich, Germany.
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23
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Kellogg CM, Pham K, Ko S, Cox JEJ, Machalinski AH, Stout MB, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Consistent specificity and efficiency of tamoxifen-mediated cre induction across ages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558482. [PMID: 37781585 PMCID: PMC10541132 DOI: 10.1101/2023.09.19.558482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Temporally controlling cre recombination through tamoxifen (Tam) induction has many advantages for biomedical research. Most studies report Tam induction at early post-natal/juvenile (<2 m.o.) mouse ages, but age-related neurodegeneration and aging studies can require cre induction in older mice (>12 m.o.). While anecdotally reported as problematic, there are no published comparisons of Tam mediated cre induction at early and late ages. Here, microglial-specific Cx3cr1 creERT 2 mice were crossed to a floxed NuTRAP reporter to compare cre induction at early (3-6 m.o.) and late (20 m.o.) ages. Specificity and efficiency of microglial labeling at 21-22 m.o. were identical in mice induced with Tam at 3-6 m.o. or 20 m.o. of age. Age-related microglial translatomic changes were also similar regardless of Tam induction age. Each cre and flox mouse line should be validated independently, however, these findings demonstrate that Tam-mediated cre induction can be performed even into older mouse ages.
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24
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Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J. Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development. Nat Commun 2023; 14:5862. [PMID: 37735176 PMCID: PMC10514308 DOI: 10.1038/s41467-023-41408-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
While the accessibility of enhancers is dynamically regulated during development, promoters tend to be constitutively accessible and poised for activation by paused Pol II. By studying Lola-I, a Drosophila zinc finger transcription factor, we show here that the promoter state can also be subject to developmental regulation independently of gene activation. Lola-I is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers and reveal a mechanism for the de novo establishment of paused Pol II at promoters.
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Affiliation(s)
- Vivekanandan Ramalingam
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center----, Kansas City, KS, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Xinyang Yu
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Michael Buck
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biomedical Informatics, Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center----, Kansas City, KS, USA.
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25
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Stuer N, Van Damme P, Goormachtig S, Van Dingenen J. Seeking the interspecies crosswalk for filamentous microbe effectors. TRENDS IN PLANT SCIENCE 2023; 28:1045-1059. [PMID: 37062674 DOI: 10.1016/j.tplants.2023.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/02/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Both pathogenic and symbiotic microorganisms modulate the immune response and physiology of their host to establish a suitable niche. Key players in mediating colonization outcome are microbial effector proteins that act either inside (cytoplasmic) or outside (apoplastic) the plant cells and modify the abundance or activity of host macromolecules. We compile novel insights into the much-disputed processes of effector secretion and translocation of filamentous organisms, namely fungi and oomycetes. We report how recent studies that focus on unconventional secretion and effector structure challenge the long-standing image of effectors as conventionally secreted proteins that are translocated with the aid of primary amino acid sequence motifs. Furthermore, we emphasize the potential of diverse, unbiased, state-of-the-art proteomics approaches in the holistic characterization of fungal and oomycete effectomes.
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Affiliation(s)
- Naomi Stuer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium.
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium.
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26
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543497. [PMID: 37333391 PMCID: PMC10274634 DOI: 10.1101/2023.06.05.543497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. This is especially true as for DNA modifications where most data are derived from bisulfite sequencing that cannot differentiate between DNA methylation and hydroxymethylation. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation of gene expression between neurons and glia. Results After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT whole genome oxidative bisulfite sequencing to assess the neuronal translatome and epigenome in the hippocampus of young mice (3 months old). These data were then compared to microglial and astrocytic data from NuTRAP models. When comparing the different cell types, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, with limited differences occurring within proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of mCG with gene expression within the gene body while a positive relationship between distal promoter and gene body hmCG and gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. Conclusions In this study, we identified differential usage of DNA modifications across CNS cell types, and assessed the relationship between DNA modifications and gene expression in neurons and glia. Despite having different global levels, the general modification-gene expression relationship was conserved across cell types. The enrichment of differential modifications in gene bodies and distal regulatory elements, but not proximal promoters, across cell types highlights epigenomic patterning in these regions as potentially greater determinants of cell identity.
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Affiliation(s)
- Kyla B. Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Sarah R. Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kevin D. Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - David R. Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Willard M. Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK USA
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27
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Debernardi JM, Burguener G, Bubb K, Liu Q, Queitsch C, Dubcovsky J. Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei. BMC PLANT BIOLOGY 2023; 23:270. [PMID: 37211599 DOI: 10.1186/s12870-023-04281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND The genetic information contained in the genome of an organism is organized in genes and regulatory elements that control gene expression. The genomes of multiple plants species have already been sequenced and the gene repertory have been annotated, however, cis-regulatory elements remain less characterized, limiting our understanding of genome functionality. These elements act as open platforms for recruiting both positive- and negative-acting transcription factors, and as such, chromatin accessibility is an important signature for their identification. RESULTS In this work we developed a transgenic INTACT [isolation of nuclei tagged in specific cell types] system in tetraploid wheat for nuclei purifications. Then, we combined the INTACT system together with the assay for transposase-accessible chromatin with sequencing [ATAC-seq] to identify open chromatin regions in wheat root tip samples. Our ATAC-seq results showed a large enrichment of open chromatin regions in intergenic and promoter regions, which is expected for regulatory elements and that is similar to ATAC-seq results obtained in other plant species. In addition, root ATAC-seq peaks showed a significant overlap with a previously published ATAC-seq data from wheat leaf protoplast, indicating a high reproducibility between the two experiments and a large overlap between open chromatin regions in root and leaf tissues. Importantly, we observed overlap between ATAC-seq peaks and cis-regulatory elements that have been functionally validated in wheat, and a good correlation between normalized accessibility and gene expression levels. CONCLUSIONS We have developed and validated an INTACT system in tetraploid wheat that allows rapid and high-quality nuclei purification from root tips. Those nuclei were successfully used to performed ATAC-seq experiments that revealed open chromatin regions in the wheat genome that will be useful to identify cis-regulatory elements. The INTACT system presented here will facilitate the development of ATAC-seq datasets in other tissues, growth stages, and under different growing conditions to generate a more complete landscape of the accessible DNA regions in the wheat genome.
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Affiliation(s)
- Juan M Debernardi
- University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - German Burguener
- University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Kerry Bubb
- Dept. of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Qiujie Liu
- University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | | | - Jorge Dubcovsky
- University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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28
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Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W, Lister R, Wolvetang EJ. Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development. Genes (Basel) 2023; 14:genes14050957. [PMID: 37239317 DOI: 10.3390/genes14050957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here, we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models even after prolonged culture, cortical neurons derived from mouse ESCs acquired in vivo levels of mCH over a similar time period in both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition was coincident with a transient increase in Dnmt3a, preceded by the postmitotic marker Rbfox3 (NeuN), was enriched at the nuclear lamina, and negatively correlated with gene expression. We further found that methylation patterning subtly differed between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional noncell autonomous processes. Our findings show that mouse ESC-derived neurons, in contrast to those of humans, can recapitulate the unique DNA methylation landscape of adult neurons in vitro over experimentally tractable timeframes, which allows their use as a model system to study epigenome maturation over development.
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Affiliation(s)
- Sally Martin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Nelly Olova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Conor O'Leary
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Elena Ivanova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Jennifer Dechka
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca K Simmons
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Helen M Cooper
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wolf Reik
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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29
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Hermawaty D, Cahn J, Lister R, Considine MJ. Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds. TREE PHYSIOLOGY 2023; 43:675-689. [PMID: 36637421 PMCID: PMC10094961 DOI: 10.1093/treephys/tpac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/17/2022] [Accepted: 12/21/2022] [Indexed: 05/03/2023]
Abstract
The regulation of DNA accessibility by histone modification has emerged as a paradigm of developmental and environmental programming. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a versatile tool to investigate in vivo protein-DNA interaction and has enabled advances in mechanistic understanding of physiologies. The technique has been successfully demonstrated in several plant species and tissues; however, it has remained challenging in woody tissues, in particular complex structures such as perennating buds. Here we developed a ChIP method specifically for mature dormant buds of grapevine (Vitis vinifera cv. Cabernet Sauvignon). Each step of the protocol was systematically optimized, including crosslinking, chromatin extraction, sonication and antibody validation. Analysis of histone H3-enriched DNA was performed to evaluate the success of the protocol and identify occupancy of histone H3 along grapevine bud chromatin. To our best knowledge, this is the first ChIP experiment protocol optimized for the grapevine bud system.
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Affiliation(s)
- Dina Hermawaty
- The UWA Institute of Agriculture, The University of Western Australia, M082/35 Striling Hwy, Perth, WA 6009, Australia
| | - Jonathan Cahn
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M310/35 Striling Hwy, Perth, WA 6009, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M310/35 Striling Hwy, Perth, WA 6009, Australia
| | - Michael J Considine
- The UWA Institute of Agriculture, The University of Western Australia, M082/35 Striling Hwy, Perth, WA 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M310/35 Striling Hwy, Perth, WA 6009, Australia
- Horticulture and Irrigated Agriculture, Department of Primary Industries and Regional Development, 1 Nash St, Perth, 6000, Australia
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30
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Boussardon C, Carrie C, Keech O. Comparing plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad133. [PMID: 37026385 PMCID: PMC10400147 DOI: 10.1093/jxb/erad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Indexed: 06/19/2023]
Abstract
Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, proplasts to only cite a few denominations. Over the past decades, methods based on density gradients and differential centrifugations have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the TOC64 gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis thaliana using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, and allowed the identification of 1672 proteins, among which 1342 were predicted plastidial, and 705 were fully confirmed according to SUBA5. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NDC1, VTE1, PGL34, ABC1K1) and cyclic electron flow in plastids originating from vascular tissues. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.
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Affiliation(s)
- Clément Boussardon
- Department of Plant Physiology, Umeå Plant Science, Umeå University, S-90187 Umeå, Sweden
| | - Chris Carrie
- School of Biological Sciences, University of Auckland, 3A Symonds St, Auckland,1142, New Zealand
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science, Umeå University, S-90187 Umeå, Sweden
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31
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Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
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32
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Pires RC, Ferro A, Capote T, Usié A, Correia B, Pinto G, Menéndez E, Marum L. Laser Microdissection of Woody and Suberized Plant Tissues for RNA-Seq Analysis. Mol Biotechnol 2023; 65:419-432. [PMID: 35976558 DOI: 10.1007/s12033-022-00542-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/05/2022] [Indexed: 10/15/2022]
Abstract
An accurate profile of gene expression at a cellular level can contribute to a better understanding of biological processes and complexities involved in regulatory mechanism of woody plants. Laser microdissection is one technique that allows isolation of specific, target cells or tissue from a heterogeneous cell population. This technique entails microscopic visualization of the selected tissue and use a laser beam to separate the desired cells from surrounding tissue. Initial identification of these cells is made based on morphology and/or histological staining. Some works have been made in several tissues and plant models. However, there are few studies of laser microdissection application in woody species, particularly, lignified and suberized cells. Moreover, the presence of high level of suberin in cell walls can be a big challenge for the application of this approach. In our study it was developed a technique for tissue isolation, using laser microdissection of four different plant cell types (phellogen, lenticels, cortex and xylem) from woody tissues of cork oak (Quercus suber), followed by RNA extraction and RNA-Seq. We tested several methodologies regarding laser microdissection, cryostat equipments, fixation treatments, duration of single-cells collection and number of isolated cells by laser microdissection and RNA extraction procedures. A simple and efficient protocol for tissue isolation by laser microdissection and RNA purification was obtained, with a final method validation of RNA-Seq analysis. The optimized methodology combining RNA-Seq for expression analysis will contribute to elucidate the molecular pathways associated with different development processes of the xylem and phellem in oaks, including the lenticular channels formation.
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Affiliation(s)
- Rita Costa Pires
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal
| | - Ana Ferro
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal.,MED - Mediterranean Institute for Agriculture, Environment and Development, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908, Beja, Portugal.,Center for Genomics and Systems Biology, New York University Abu Dhabi, NYUAD Campus, 129188, Abu Dhabi, United Arab Emirates
| | - Tiago Capote
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal.,MED - Mediterranean Institute for Agriculture, Environment and Development, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908, Beja, Portugal.,Center for Genomics and Systems Biology, New York University Abu Dhabi, NYUAD Campus, 129188, Abu Dhabi, United Arab Emirates
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal.,MED - Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908, Beja, Portugal
| | - Bárbara Correia
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal.,B-hive Innovations Ltd., Boole Technology Centre, Beevor Street, Lincoln, LN6 7DJ, UK
| | - Glória Pinto
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193, Aveiro, Portugal
| | - Esther Menéndez
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, Institute for Advanced Studies and Research (IIFA), University of Évora, Polo da Mitra, Ap. 94, 7006-554, Évora, Portugal.,Department of Microbiology and Genetics/CIALE, Universidad de Salamanca, 37007, Salamanca, Spain
| | - Liliana Marum
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), 7801-908, Beja, Portugal. .,MED - Mediterranean Institute for Agriculture, Environment and Development & CHANGE - Global Change and Sustainability Institute, CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908, Beja, Portugal.
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33
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Feng X, Pan S, Tu H, Huang J, Xiao C, Shen X, You L, Zhao X, Chen Y, Xu D, Qu X, Hu H. IQ67 DOMAIN protein 21 is critical for indentation formation in pavement cell morphogenesis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:721-738. [PMID: 36263896 DOI: 10.1111/jipb.13393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/15/2022] [Indexed: 05/26/2023]
Abstract
In plants, cortical microtubules anchor to the plasma membrane in arrays and play important roles in cell shape. However, the molecular mechanism of microtubule binding proteins, which connect the plasma membrane and cortical microtubules in cell morphology remains largely unknown. Here, we report that a plasma membrane and microtubule dual-localized IQ67 domain protein, IQD21, is critical for cotyledon pavement cell (PC) morphogenesis in Arabidopsis. iqd21 mutation caused increased indentation width, decreased lobe length, and similar lobe number of PCs, whereas IQD21 overexpression had a different effect on cotyledon PC shape. Weak overexpression led to increased lobe number, decreased indentation width, and similar lobe length, while moderate or great overexpression resulted in decreased lobe number, indentation width, and lobe length of PCs. Live-cell observations revealed that IQD21 accumulation at indentation regions correlates with lobe initiation and outgrowth during PC development. Cell biological and genetic approaches revealed that IQD21 promotes transfacial microtubules anchoring to the plasma membrane via its polybasic sites and bundling at the indentation regions in both periclinal and anticlinal walls. IQD21 controls cortical microtubule organization mainly through promoting Katanin 1-mediated microtubule severing during PC interdigitation. These findings provide the genetic evidence that transfacial microtubule arrays play a determinant role in lobe formation, and the insight into the molecular mechanism of IQD21 in transfacial microtubule organization at indentations and puzzle-shaped PC development.
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Affiliation(s)
- Xinhua Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shujuan Pan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junjie Huang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430070, China
| | - Chuanlei Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyan Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yongqiang Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Danyun Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaolu Qu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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34
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Reynoso MA, Blanco FA, Zanetti ME. Nuclear and cytoplasmic lncRNAs in root tips of the model legume Medicago truncatula under control and submergence. IUBMB Life 2023. [PMID: 36852968 DOI: 10.1002/iub.2712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/21/2023] [Indexed: 03/01/2023]
Abstract
In this study, we aimed to identify long noncoding RNAs (lncRNAs) in root tips of the model legume Medicago truncatula using previously generated nuclear, total polyA, ribosome-associated polyA, and Riboseq RNA datasets, which might shed light on their localization and potential regulatory roles. RNA-seq data were mapped to the version 5 of the M. truncatula A17 genome and analyzed to identify genome annotated lncRNAs and putative new root tip (NRT) lncRNAs. lncRNAs were classified according to their genomic location relative to chromatin accessible regions, protein-coding genes and transposable elements (TE), finding differences between annotated lncRNAs and NRT lncRNAs, both in their genomic position as well as in the type of TEs in their vicinity. We investigated their response to submergence and found a set of regulated lncRNAs that were preferentially upregulated in the nucleus, some of which were located nearby genes of the conserved submergence upregulated gene families, and chromatin accessible regions suggesting a potential regulatory role. Finally, the accumulation of lncRNAs under submergence was validated by reverse transcription quantitative polymerase chain reaction on nuclear RNA, providing additional evidence of their localization, which could ultimately be required for their function.
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Affiliation(s)
- Mauricio A Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.,Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, USA
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
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35
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van Ekelenburg YS, Hornslien KS, Van Hautegem T, Fendrych M, Van Isterdael G, Bjerkan KN, Miller JR, Nowack MK, Grini PE. Spatial and temporal regulation of parent-of-origin allelic expression in the endosperm. PLANT PHYSIOLOGY 2023; 191:986-1001. [PMID: 36437711 PMCID: PMC9922421 DOI: 10.1093/plphys/kiac520] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Paul E Grini
- Authors for correspondence: E-mail: (P.E.G.), (K.S.H.)
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36
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Bhattacharyya S, Kollipara RK, Orquera-Tornakian G, Goetsch S, Zhang M, Perry C, Li B, Shelton JM, Bhakta M, Duan J, Xie Y, Xiao G, Evers BM, Hon GC, Kittler R, Munshi NV. Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm. J Clin Invest 2023; 133:e153635. [PMID: 36454649 PMCID: PMC9888383 DOI: 10.1172/jci153635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Comprehensive cis-regulatory landscapes are essential for accurate enhancer prediction and disease variant mapping. Although cis-regulatory element (CRE) resources exist for most tissues and organs, many rare - yet functionally important - cell types remain overlooked. Despite representing only a small fraction of the heart's cellular biomass, the cardiac conduction system (CCS) unfailingly coordinates every life-sustaining heartbeat. To globally profile the mouse CCS cis-regulatory landscape, we genetically tagged CCS component-specific nuclei for comprehensive assay for transposase-accessible chromatin-sequencing (ATAC-Seq) analysis. Thus, we established a global CCS-enriched CRE database, referred to as CCS-ATAC, as a key resource for studying CCS-wide and component-specific regulatory functions. Using transcription factor (TF) motifs to construct CCS component-specific gene regulatory networks (GRNs), we identified and independently confirmed several specific TF sub-networks. Highlighting the functional importance of CCS-ATAC, we also validated numerous CCS-enriched enhancer elements and suggested gene targets based on CCS single-cell RNA-Seq data. Furthermore, we leveraged CCS-ATAC to improve annotation of existing human variants related to cardiac rhythm and nominated a potential enhancer-target pair that was dysregulated by a specific SNP. Collectively, our results established a CCS-regulatory compendium, identified novel CCS enhancer elements, and illuminated potential functional associations between human genomic variants and CCS component-specific CREs.
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Affiliation(s)
| | | | | | - Sean Goetsch
- Department of Internal Medicine, Division of Cardiology
| | - Minzhe Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Cameron Perry
- Department of Internal Medicine, Division of Cardiology
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | | | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Bret M. Evers
- Department of Internal Medicine, Division of Cardiology
| | - Gary C. Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
- Department of Bioinformatics
- Hamon Center for Regenerative Science and Medicine, and
| | - Ralf Kittler
- McDermott Center for Human Growth and Development
| | - Nikhil V. Munshi
- Department of Internal Medicine, Division of Cardiology
- McDermott Center for Human Growth and Development
- Hamon Center for Regenerative Science and Medicine, and
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, USA
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37
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Gui S, Martinez-Rivas FJ, Wen W, Meng M, Yan J, Usadel B, Fernie AR. Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:446-459. [PMID: 36534120 DOI: 10.1111/tpj.16070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.
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Affiliation(s)
- Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghui Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, BioSc, 52428, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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38
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Xu X, Jackson D. Single-cell analysis opens a goldmine for plant functional studies. Curr Opin Biotechnol 2023; 79:102858. [PMID: 36493588 DOI: 10.1016/j.copbio.2022.102858] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
Functional studies in biology require the identification of genes, regulatory elements, and networks, followed by a deep understanding of how they orchestrate to specify cell types, mediate signaling, and respond to internal and external cues over evolutionary timescales. Advances in single-cell analysis have enabled biologists to tackle these questions at the resolution of the individual cell. Here, we highlight recent studies in plants that have embraced single-cell analyses to facilitate functional studies. This review will provide guidance and perspectives for incorporating these advanced approaches in plant research for the coming decades.
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Affiliation(s)
- Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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39
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Boussardon C, Keech O. Tissue-Specific Isolation of Tagged Arabidopsis Plastids. Curr Protoc 2023; 3:e673. [PMID: 36799650 DOI: 10.1002/cpz1.673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids.
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Affiliation(s)
- Clément Boussardon
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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40
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Raus AM, Fuller TD, Nelson NE, Valientes DA, Bayat A, Ivy AS. Early-life exercise primes the murine neural epigenome to facilitate gene expression and hippocampal memory consolidation. Commun Biol 2023; 6:18. [PMID: 36611093 PMCID: PMC9825372 DOI: 10.1038/s42003-022-04393-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
Aerobic exercise is well known to promote neuroplasticity and hippocampal memory. In the developing brain, early-life exercise (ELE) can lead to persistent improvements in hippocampal function, yet molecular mechanisms underlying this phenomenon have not been fully explored. In this study, transgenic mice harboring the "NuTRAP" (Nuclear tagging and Translating Ribosome Affinity Purification) cassette in Emx1 expressing neurons ("Emx1-NuTRAP" mice) undergo ELE during adolescence. We then simultaneously isolate and sequence translating mRNA and nuclear chromatin from single hippocampal homogenates containing Emx1-expressing neurons. This approach allowed us to couple translatomic with epigenomic sequencing data to evaluate the influence of histone modifications H4K8ac and H3K27me3 on translating mRNA after ELE. A subset of ELE mice underwent a hippocampal learning task to determine the gene expression and epigenetic underpinnings of ELE's contribution to improved hippocampal memory performance. From this experiment, we discover gene expression - histone modification relationships that may play a critical role in facilitated memory after ELE. Our data reveal candidate gene-histone modification interactions and implicate gene regulatory pathways involved in ELE's impact on hippocampal memory.
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Affiliation(s)
- Anthony M Raus
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Tyson D Fuller
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Nellie E Nelson
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - David A Valientes
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Anita Bayat
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Autumn S Ivy
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Neurobiology/Behavior, University of California- Irvine School of Biological Sciences, Irvine, CA, USA.
- Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Division of Neurology, Children's Hospital Orange County, Orange, CA, USA.
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41
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You Y, Koczyk G, Nuc M, Morbitzer R, Holmes DR, von Roepenack-Lahaye E, Hou S, Giudicatti A, Gris C, Manavella PA, Noël LD, Krajewski P, Lahaye T. The eINTACT system dissects bacterial exploitation of plant osmosignalling to enhance virulence. NATURE PLANTS 2023; 9:128-141. [PMID: 36550363 PMCID: PMC9873569 DOI: 10.1038/s41477-022-01302-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Bacteria inject effector proteins into host cells to manipulate cellular processes that promote disease. Since bacteria deliver minuscule amounts of effectors only into targeted host cells, it is technically challenging to capture effector-dependent cellular changes from bulk-infected host tissues. Here, we report a new technique called effector-inducible isolation of nuclei tagged in specific cell types (eINTACT), which facilitates affinity-based purification of nuclei from Arabidopsis plant cells that have received Xanthomonas bacterial effectors. Analysis of purified nuclei reveals that the Xanthomonas effector XopD manipulates the expression of Arabidopsis abscisic acid signalling-related genes and activates OSCA1.1, a gene encoding a calcium-permeable channel required for stomatal closure in response to osmotic stress. The loss of OSCA1.1 causes leaf wilting and reduced bacterial growth in infected leaves, suggesting that OSCA1.1 promotes host susceptibility. eINTACT allows us to uncover that XopD exploits host OSCA1.1/abscisic acid osmosignalling-mediated stomatal closure to create a humid habitat that favours bacterial growth and opens up a new avenue for accurately elucidating functions of effectors from numerous gram-negative plant bacteria in native infection contexts.
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Affiliation(s)
- Yuan You
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany.
| | - Grzegorz Koczyk
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Maria Nuc
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Robert Morbitzer
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Danalyn R Holmes
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
| | | | - Shiji Hou
- State Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR of China
| | - Axel Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Carine Gris
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Laurent D Noël
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Thomas Lahaye
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
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Gramma V, Wahl V. RNA In Situ Hybridization on Plant Tissue Sections: Expression Analysis at Cellular Resolution. Methods Mol Biol 2023; 2686:331-350. [PMID: 37540368 DOI: 10.1007/978-1-0716-3299-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
RNA in situ hybridization offers a means to study the spatial expression of candidate genes by making use of specific, labelled RNA probes on thin tissue sections. Unlike other methods, such as promoter GUS fusions, for which all regulatory sequences should be available and transgenic plants have to be generated, RNA in situ hybridization allows specific and direct detection of even low abundant transcripts at cellular resolution. Although various protocols exist, the results published throughout the literature indicate a very obvious problem of the technique: each step has the potential to affect the outcome, that is, the signal strength, presence or absence of background, and visibility of individual cells. The protocol described here tries to avoid all these problems by addressing each step in detail and providing advice regarding critical steps for a distinct visualization of gene expression on intact tissue sections without any background.
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Affiliation(s)
| | - Vanessa Wahl
- Max Planck Institute of Plant Physiology, Potsdam, Germany.
- The James Hutton Institute, Dundee, UK.
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43
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He S, Feng X. DNA methylation dynamics during germline development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2240-2251. [PMID: 36478632 PMCID: PMC10108260 DOI: 10.1111/jipb.13422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.
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Affiliation(s)
- Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, College of AgricultureSouth China Agricultural UniversityGuangzhou510642China
| | - Xiaoqi Feng
- John Innes Centre, Colney LaneNorwichNR4 7UHUK
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44
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Chucair-Elliott AJ, Ocañas SR, Pham K, Van Der Veldt M, Cheyney A, Stanford D, Gurley J, Elliott MH, Freeman WM. Translatomic response of retinal Müller glia to acute and chronic stress. Neurobiol Dis 2022; 175:105931. [PMID: 36423879 PMCID: PMC9875566 DOI: 10.1016/j.nbd.2022.105931] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Analysis of retina cell type-specific epigenetic and transcriptomic signatures is crucial to understanding the pathophysiology of retinal degenerations such as age-related macular degeneration (AMD) and delineating cell autonomous and cell-non-autonomous mechanisms. We have discovered that Aldh1l1 is specifically expressed in the major macroglia of the retina, Müller glia, and, unlike the brain, is not expressed in retinal astrocytes. This allows use of Aldh1l1 cre drivers and Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) constructs for temporally controlled labeling and paired analysis of Müller glia epigenomes and translatomes. As validated through a variety of approaches, the Aldh1l1cre/ERT2-NuTRAP model provides Müller glia specific translatomic and epigenomic profiles without the need to isolate whole cells. Application of this approach to models of acute injury (optic nerve crush) and chronic stress (aging) uncovered few common Müller glia-specific transcriptome changes in inflammatory pathways, and mostly differential signatures for each stimulus. The expression of members of the IL-6 and integrin-linked kinase signaling pathways was enhanced in Müller glia in response to optic nerve crush but not aging. Unique changes in neuroinflammation and fibrosis signaling pathways were observed in response to aging but not with optic nerve crush. The Aldh1l1cre/ERT2-NuTRAP model allows focused molecular analyses of a single, minority cell type within the retina, providing more substantial effect sizes than whole tissue analyses. The NuTRAP model, nucleic acid isolation, and validation approaches presented here can be applied to any retina cell type for which a cell type-specific cre is available.
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Affiliation(s)
- Ana J. Chucair-Elliott
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Corresponding authors at: Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. (A.J. Chucair-Elliott), (W.M. Freeman)
| | - Sarah R. Ocañas
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael Van Der Veldt
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Ashley Cheyney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David Stanford
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Jami Gurley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael H. Elliott
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M. Freeman
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA,Corresponding authors at: Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. (A.J. Chucair-Elliott), (W.M. Freeman)
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45
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Kim ED, Dorrity MW, Fitzgerald BA, Seo H, Sepuru KM, Queitsch C, Mitsuda N, Han SK, Torii KU. Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment. NATURE PLANTS 2022; 8:1453-1466. [PMID: 36522450 PMCID: PMC9788986 DOI: 10.1038/s41477-022-01304-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/28/2022] [Indexed: 05/12/2023]
Abstract
Chromatin architecture and transcription factor (TF) binding underpin cell-fate specification during development, but their mutual regulatory relationships remain unclear. Here we report an atlas of dynamic chromatin landscapes during stomatal cell-lineage progression, in which sequential cell-state transitions are governed by lineage-specific bHLH TFs. Major reprogramming of chromatin accessibility occurs at the proliferation-to-differentiation transition. We discover novel co-cis regulatory elements (CREs) signifying the early precursor stage, BBR/BPC (GAGA) and bHLH (E-box) motifs, where master-regulatory bHLH TFs, SPEECHLESS and MUTE, consecutively bind to initiate and terminate the proliferative state, respectively. BPC TFs complex with MUTE to repress SPEECHLESS expression through a local deposition of repressive histone marks. We elucidate the mechanism by which cell-state-specific heterotypic TF complexes facilitate cell-fate commitment by recruiting chromatin modifiers via key co-CREs.
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Affiliation(s)
- Eun-Deok Kim
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bridget A Fitzgerald
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hyemin Seo
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Krishna Mohan Sepuru
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Soon-Ki Han
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan.
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46
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Raus AM, Nelson NE, Fuller TD, Ivy AS. "SIT" with Emx1-NuTRAP Mice: Simultaneous INTACT and TRAP for Paired Transcriptomic and Epigenetic Sequencing. Curr Protoc 2022; 2:e570. [PMID: 36287035 PMCID: PMC9614570 DOI: 10.1002/cpz1.570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Epigenetic regulation of transcription is gaining increasing importance in the study of neurobiology. The advent of sequencing technology has enabled the study of this regulation across the entire genome and transcriptome. However, modern methods that allow the correlation of transcriptomic data with epigenomic regulation have had several key limitations, including use of separate tissue sources and detection of low-expression genes. This article describes a method combining isolation of nuclei tagged in specific cell types (INTACT) with translating ribosome affinity purification (TRAP) in the same cell homogenate, referred to as Simultaneous INTACT and TRAP (SIT). We used this technical approach to directly couple transcriptomic sequencing with epigenomic data in neurons derived from the mouse hippocampus. We demonstrate this method with an Emx1-NuTRAP transgenic mouse model. Here, we present protocols for SIT and for the generation and validation of the Emx1-NuTRAP mouse model that we used to demonstrate SIT. These methods enable cell type-specific comparison of translating mRNA and chromatin data from the same set of cells. Using SIT and the Emx1-NuTRAP transgenic mouse model, researchers can compare epigenomic data to transcriptomic data in the same set of hippocampal excitatory neurons. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Emx1-NuTRAP transgenic mouse line for labeling excitatory neurons in the hippocampus Basic Protocol 2: SIT: Simultaneous Isolation of nuclei tagged in specific cell types (INTACT) and Translating ribosome affinity purification (TRAP).
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Affiliation(s)
- Anthony M Raus
- Physiology and Biophysics, University of California, Irvine, School of Medicine, Irvine, California
| | - Nellie E Nelson
- Physiology and Biophysics, University of California, Irvine, School of Medicine, Irvine, California
| | - Tyson D Fuller
- Pediatrics, University of California, Irvine, School of Medicine, Irvine, California
| | - Autumn S Ivy
- Physiology and Biophysics, University of California, Irvine, School of Medicine, Irvine, California.,Pediatrics, University of California, Irvine, School of Medicine, Irvine, California.,Anatomy and Neurobiology, University of California, Irvine, School of Medicine, Irvine, California.,Division of Neurology, Children's Hospital Orange County, Orange, California
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47
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Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022; 17:1518-1552. [PMID: 35478247 PMCID: PMC9189070 DOI: 10.1038/s41596-022-00692-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment.
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Affiliation(s)
- Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lucas Kampman
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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48
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Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death. Cell Host Microbe 2022; 30:944-960.e8. [PMID: 35654045 DOI: 10.1016/j.chom.2022.05.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/07/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022]
Abstract
The intestinal microbiome releases a plethora of small molecules. Here, we show that the Ruminococcaceae metabolite isoamylamine (IAA) is enriched in aged mice and elderly people, whereas Ruminococcaceae phages, belonging to the Myoviridae family, are reduced. Young mice orally administered IAA show cognitive decline, whereas Myoviridae phage administration reduces IAA levels. Mechanistically, IAA promotes apoptosis of microglial cells by recruiting the transcriptional regulator p53 to the S100A8 promoter region. Specifically, IAA recognizes and binds the S100A8 promoter region to facilitate the unwinding of its self-complementary hairpin structure, thereby subsequently enabling p53 to access the S100A8 promoter and enhance S100A8 expression. Thus, our findings provide evidence that small molecules released from the gut microbiome can directly bind genomic DNA and act as transcriptional coregulators by recruiting transcription factors. These findings further unveil a molecular mechanism that connects gut metabolism to gene expression in the brain with implications for disease development.
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49
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Neumann M, Xu X, Smaczniak C, Schumacher J, Yan W, Blüthgen N, Greb T, Jönsson H, Traas J, Kaufmann K, Muino JM. A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data. Nat Commun 2022; 13:2838. [PMID: 35595749 PMCID: PMC9122980 DOI: 10.1038/s41467-022-30177-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
Cellular heterogeneity in growth and differentiation results in organ patterning. Single-cell transcriptomics allows characterization of gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during this methodology. To recover the original location of cells in the developing organ is essential to link gene activity with cellular identity and function in plants. Here, we propose a method to reconstruct genome-wide gene expression patterns of individual cells in a 3D flower meristem by combining single-nuclei RNA-seq with microcopy-based 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the method is used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com. Single-cell transcriptomics allows gene expression heterogeneity to be assessed at cellular resolution but the original location of each cell is unknown. Here the authors combine single nuclei RNA-seq with 3D spatial reconstruction of floral meristems to link gene activities with morphology.
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Affiliation(s)
- Manuel Neumann
- Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Xiaocai Xu
- Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Cezary Smaczniak
- Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Julia Schumacher
- Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Wenhao Yan
- Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Thomas Greb
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Henrik Jönsson
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Jan Traas
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon, INRAE, CNRS, UCBL, 69364, Lyon, France
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany
| | - Jose M Muino
- Systems Biology of Gene Regulation, Humboldt-Universität zu Berlin, Institute of Biology, Berlin, Germany.
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Van der Ent MA, Svilar D, Cleuren AC. Molecular analysis of vascular gene expression. Res Pract Thromb Haemost 2022; 6:e12718. [PMID: 35599705 PMCID: PMC9118339 DOI: 10.1002/rth2.12718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
A State of the Art lecture entitled "Molecular Analysis of Vascular Gene Expression" was presented at the ISTH Congress in 2021. Endothelial cells (ECs) form a critical interface between the blood and underlying tissue environment, serving as a reactive barrier to maintain tissue homeostasis. ECs play an important role in not only coagulation, but also in the response to inflammation by connecting these two processes in the host defense against pathogens. Furthermore, ECs tailor their behavior to the needs of the microenvironment in which they reside, resulting in a broad display of EC phenotypes. While this heterogeneity has been acknowledged for decades, the contributing molecular mechanisms have only recently started to emerge due to technological advances. These include high-throughput sequencing combined with methods to isolate ECs directly from their native tissue environment, as well as sequencing samples at a high cellular resolution. In addition, the newest technologies simultaneously quantitate and visualize a multitude of RNA transcripts directly in tissue sections, thus providing spatial information. Understanding how ECs function in (patho)physiological conditions is crucial to develop new therapeutics as many diseases can directly affect the endothelium. Of particular relevance for thrombotic disorders, EC dysfunction can lead to a procoagulant, proinflammatory phenotype with increased vascular permeability that can result in coagulopathy and tissue damage, as seen in a number of infectious diseases, including sepsis and coronavirus disease 2019. In light of the current pandemic, we will summarize relevant new data on the latter topic presented during the 2021 ISTH Congress.
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Affiliation(s)
| | - David Svilar
- Department of PediatricsUniversity of MichiganAnn ArborMichiganUSA
- Life Sciences InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Audrey C.A. Cleuren
- Life Sciences InstituteUniversity of MichiganAnn ArborMichiganUSA
- Cardiovascular Biology Research ProgramOklahoma Medical Research FoundationOklahoma CityOklahomaUSA
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