1
|
Barakate A, Orr J, Schreiber M, Colas I, Lewandowska D, McCallum N, Macaulay M, Morris J, Arrieta M, Hedley PE, Ramsay L, Waugh R. Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I. Front Plant Sci 2021; 11:619404. [PMID: 33510760 PMCID: PMC7835676 DOI: 10.3389/fpls.2020.619404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/15/2020] [Indexed: 05/07/2023]
Abstract
In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene-zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I-tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.
Collapse
Affiliation(s)
- Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jamie Orr
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | | | - Nicola McCallum
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Mikel Arrieta
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- School of Agriculture and Wine, University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
2
|
Barra L, Termolino P, Aiese Cigliano R, Cremona G, Paparo R, Lanzillo C, Consiglio MF, Conicella C. Meiocyte Isolation by INTACT and Meiotic Transcriptome Analysis in Arabidopsis. Front Plant Sci 2021; 12:638051. [PMID: 33747019 PMCID: PMC7969724 DOI: 10.3389/fpls.2021.638051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/01/2021] [Indexed: 05/06/2023]
Abstract
Isolation of nuclei tagged in specific cell types (INTACT) is a method developed to isolate cell-type-specific nuclei that are tagged through in vivo biotin labeling of a nuclear targeting fusion (NTF) protein. In our work, INTACT was used to capture nuclei of meiocytes and to generate a meiotic transcriptome in Arabidopsis. Using the promoter of AtDMC1 recombinase to label meiotic nuclei, we generated transgenic plants carrying AtDMC1:NTF along with biotin ligase enzyme (BirA) under the constitutive ACTIN2 (ACT2) promoter. AtDMC1-driven expression of biotin-labeled NTF allowed us to collect nuclei of meiocytes by streptavidin-coated magnetic beads. The nuclear meiotic transcriptome was obtained by RNA-seq using low-quantity input RNA. Transcripts grouped into different categories according to their expression levels were investigated by gene ontology enrichment analysis (GOEA). The most enriched GO term "DNA demethylation" in mid/high-expression classes suggests that this biological process is particularly relevant to meiosis onset. The majority of genes with established roles in meiosis were distributed in the classes of mid/high and high expression. Meiotic transcriptome was compared with public available transcriptomes from other tissues in Arabidopsis. Bioinformatics analysis by expression network identified a core of more than 1,500 genes related to meiosis landmarks.
Collapse
Affiliation(s)
- Lucia Barra
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, Italy
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, Italy
| | | | - Gaetana Cremona
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, Italy
| | - Rosa Paparo
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, Italy
| | - Carmine Lanzillo
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, Italy
| | | | - Clara Conicella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Portici, Italy
- *Correspondence: Clara Conicella,
| |
Collapse
|
3
|
Chang P, Tseng YF, Chen PY, Wang CJR. Using Flow Cytometry to Isolate Maize Meiocytes for Next Generation Sequencing: A Time and Labor Efficient Method. ACTA ACUST UNITED AC 2018; 3:e20068. [PMID: 29927118 DOI: 10.1002/cppb.20068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Meiosis is essential during sexual reproduction to generate haploid gametes. Genomic or epigenomic studies of meiosis in multicellular organisms using next-generation sequencing (NGS) methods have been limited because of the difficulty of collecting thousands to millions of meiocytes. Here, we describe a simple protocol to efficiently isolate maize male meiocytes from formaldehyde-fixed samples for NGS techniques that require chemical crosslinking to preserve complex interactions or chromatin architecture. Anthers at desired meiotic stages are selected, fixed with paraformaldehyde, and disrupted using a homogenizer. Cell walls are digested to produce a cell suspension containing small somatic cells and large individual meiocytes. The meiocyte fraction is enriched by size separation with cell strainers and further purified by flow cytometry. From 400 anthers, we can isolate 20,000 meiocytes at 98% purity in 6 to 8 hours. © 2018 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Fang Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | |
Collapse
|