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Article ; Online: Exploring the identity of individual plant cells in space and time.

Oliva, Marina / Lister, Ryan

2023 Volume 240, Issue 1, Page(s) 61–67

Abstract: In recent years, single-cell genomics, coupled to imaging techniques, have become the state-of-the-art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity ... ...

Abstract	In recent years, single-cell genomics, coupled to imaging techniques, have become the state-of-the-art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity of data on cell identity at an unprecedented resolution, but what biological insights can be gained from such data sets? Using recently published studies in plant sciences, we will highlight how single-cell technologies have enabled a better comprehension of tissue organisation, cell fate dynamics in development or in response to various stimuli, as well as identifying key transcriptional regulators of cell identity. We discuss the limitations and technical hurdles to overcome, as well as future directions, and the promising use of single-cell omics to understand, predict, and manipulate plant development and physiology.
MeSH term(s)	Plant Cells ; Genomics/methods ; Cell Differentiation ; Plants/genetics
Language	English
Publishing date	2023-07-22
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19153
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Article ; Online: Exploring the identity of individual plant cells in space and time

Oliva, Marina / Lister, Ryan

New Phytologist. 2023 Oct., v. 240, no. 1 p.61-67

2023

Abstract: In recent years, single‐cell genomics, coupled to imaging techniques, have become the state‐of‐the‐art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity ... ...

Abstract	In recent years, single‐cell genomics, coupled to imaging techniques, have become the state‐of‐the‐art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity of data on cell identity at an unprecedented resolution, but what biological insights can be gained from such data sets? Using recently published studies in plant sciences, we will highlight how single‐cell technologies have enabled a better comprehension of tissue organisation, cell fate dynamics in development or in response to various stimuli, as well as identifying key transcriptional regulators of cell identity. We discuss the limitations and technical hurdles to overcome, as well as future directions, and the promising use of single‐cell omics to understand, predict, and manipulate plant development and physiology.
Keywords	genomics ; plant development ; space and time ; transcription (genetics)
Language	English
Dates of publication	2023-10
Size	p. 61-67.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	REVIEW
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19153
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Epigenome plasticity in plants.

Lloyd, James P B / Lister, Ryan

Nature reviews. Genetics

2021 Volume 23, Issue 1, Page(s) 55–68

Abstract: Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant ... ...

Abstract	Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
MeSH term(s)	DNA Methylation ; Epigenesis, Genetic/genetics ; Epigenome/genetics ; Epigenomics ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genetic Variation ; Models, Genetic ; Mutation ; Plant Proteins/genetics ; Plants/classification ; Plants/genetics ; Transcription Initiation Site
Chemical Substances	Plant Proteins
Language	English
Publishing date	2021-09-15
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/s41576-021-00407-y
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Article ; Online: Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9.

Nguyen, Trung Viet / Lister, Ryan

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2272, Page(s) 181–194

Abstract: Methylation of DNA at cytosine bases is an important DNA modification underlying normal development and disease states. Despite decades of research into the biological function of DNA methylation, most of the observations so far have relied primarily on ... ...

Abstract	Methylation of DNA at cytosine bases is an important DNA modification underlying normal development and disease states. Despite decades of research into the biological function of DNA methylation, most of the observations so far have relied primarily on associative data between observed changes in DNA methylation states and local changes in transcriptional activity or chromatin state processes. This is primarily due to the lack of molecular tools to precisely modify DNA methylation in the genome. Recent advances in genome editing technologies have allowed repurposing the CRISPR-Cas9 system for epigenome editing by fusing the catalytically dead Cas9 (dCas9) to epigenome modifying enzymes. Moreover, methods of recruiting multiple protein domains, including the SunTag system, have increased the efficacy of epigenome editing at target sites. Here, we describe an end-to-end protocol for efficient targeted removal of DNA methylation by recruiting multiple catalytic domain of TET1 enzymes to the target sites with the dCas9-SunTag system, including sgRNA design, molecular cloning, delivery of plasmid into mammalian cells, and targeted DNA methylation analysis.
MeSH term(s)	CRISPR-Cas Systems ; Chromatin ; Computational Biology/methods ; DNA/analysis ; DNA/chemistry ; DNA/genetics ; DNA Demethylation ; Epigenesis, Genetic ; Gene Editing ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Mixed Function Oxygenases/antagonists & inhibitors ; Mixed Function Oxygenases/genetics ; Mixed Function Oxygenases/metabolism ; Oxidation-Reduction ; Promoter Regions, Genetic ; Proto-Oncogene Proteins/antagonists & inhibitors ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; Sulfites/chemistry
Chemical Substances	Chromatin ; Proto-Oncogene Proteins ; Sulfites ; DNA (9007-49-2) ; Mixed Function Oxygenases (EC 1.-) ; TET1 protein, human (EC 1.-) ; hydrogen sulfite (OJ9787WBLU)
Language	English
Publishing date	2021-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1294-1_10
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Article ; Online: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.

Nobori, Tatsuya / Oliva, Marina / Lister, Ryan / Ecker, Joseph R

Nature plants

2023 Volume 9, Issue 7, Page(s) 1026–1033

Abstract: Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (plant hybridization-based targeted observation of gene expression ... ...

Abstract	Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (plant hybridization-based targeted observation of gene expression map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyse 28 cell-type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-sequencing datasets in complex plant tissue.
MeSH term(s)	In Situ Hybridization, Fluorescence/methods ; Plants/genetics ; Arabidopsis/genetics ; Gene Expression Profiling/methods
Language	English
Publishing date	2023-06-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2055-0278
ISSN (online)	2055-0278
DOI	10.1038/s41477-023-01439-4
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Article ; Online: Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds.

Hermawaty, Dina / Cahn, Jonathan / Lister, Ryan / Considine, Michael J

Tree physiology

2023 Volume 43, Issue 4, Page(s) 675–689

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 ... ...

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.
MeSH term(s)	Chromatin Immunoprecipitation Sequencing ; Histones/genetics ; Wood ; Chromatin ; Vitis/genetics
Chemical Substances	Histones ; Chromatin
Language	English
Publishing date	2023-01-17
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	743341-4
ISSN	1758-4469 ; 0829-318X
ISSN (online)	1758-4469
ISSN	0829-318X
DOI	10.1093/treephys/tpac146
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Article ; Online: Evaluating the effect of inequalities in oral anti-coagulant prescribing on outcomes in people with atrial fibrillation.

Mulholland, Ryan J / Manca, Francesco / Ciminata, Giorgio / Quinn, Terry J / Trotter, Robert / Pollock, Kevin G / Lister, Steven / Geue, Claudia

European heart journal open

2024 Volume 4, Issue 2, Page(s) oeae016

Abstract: Aims: Whilst anti-coagulation is typically recommended for thromboprophylaxis in atrial fibrillation (AF), it is often never prescribed or prematurely discontinued. The aim of this study was to evaluate the effect of inequalities in anti-coagulant ... ...

Abstract	Aims: Whilst anti-coagulation is typically recommended for thromboprophylaxis in atrial fibrillation (AF), it is often never prescribed or prematurely discontinued. The aim of this study was to evaluate the effect of inequalities in anti-coagulant prescribing by assessing stroke/systemic embolism (SSE) and bleeding risk in people with AF who continue anti-coagulation compared with those who stop transiently, permanently, or never start. Methods and results: This retrospective cohort study utilized linked Scottish healthcare data to identify adults diagnosed with AF between January 2010 and April 2016, with a CHA Conclusion: Our data suggest significant inequalities in anti-coagulation prescribing, with substantial opportunity to improve initiation and continuation. Decision-making should be patient-centred and must recognize that discontinuation or cessation is associated with considerable thromboembolic risk not offset by mitigated bleeding risk.
Language	English
Publishing date	2024-03-05
Publishing country	England
Document type	Journal Article
ISSN	2752-4191
ISSN (online)	2752-4191
DOI	10.1093/ehjopen/oeae016
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Article ; Online: A modular dCas9-based recruitment platform for combinatorial epigenome editing.

Swain, Tessa / Pflueger, Christian / Freytag, Saskia / Poppe, Daniel / Pflueger, Jahnvi / Nguyen, Trung Viet / Li, Ji Kevin / Lister, Ryan

Nucleic acids research

2024 Volume 52, Issue 1, Page(s) 474–491

Abstract: Targeted epigenome editing tools allow precise manipulation and investigation of genome modifications, however they often display high context dependency and variable efficacy between target genes and cell types. While systems that simultaneously recruit ...

Abstract	Targeted epigenome editing tools allow precise manipulation and investigation of genome modifications, however they often display high context dependency and variable efficacy between target genes and cell types. While systems that simultaneously recruit multiple distinct 'effector' chromatin regulators can improve efficacy, they generally lack control over effector composition and spatial organisation. To overcome this we have created a modular combinatorial epigenome editing platform, called SSSavi. This system is an interchangeable and reconfigurable docking platform fused to dCas9 that enables simultaneous recruitment of up to four different effectors, allowing precise control of effector composition and spatial ordering. We demonstrate the activity and specificity of the SSSavi system and, by testing it against existing multi-effector targeting systems, demonstrate its comparable efficacy. Furthermore, we demonstrate the importance of the spatial ordering of the recruited effectors for effective transcriptional regulation. Together, the SSSavi system enables exploration of combinatorial effector co-recruitment to enhance manipulation of chromatin contexts previously resistant to targeted editing.
MeSH term(s)	Chromatin/genetics ; CRISPR-Cas Systems ; Epigenesis, Genetic ; Epigenome ; Gene Editing/methods ; Gene Expression Regulation
Chemical Substances	Chromatin
Language	English
Publishing date	2024-01-24
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1108
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Article ; Online: schex avoids overplotting for large single-cell RNA-sequencing datasets.

Freytag, Saskia / Lister, Ryan

Bioinformatics (Oxford, England)

2019 Volume 36, Issue 7, Page(s) 2291–2292

Abstract: Summary: Due to the scale and sparsity of single-cell RNA-sequencing data, traditional plots can obscure vital information. Our R package schex overcomes this by implementing hexagonal binning, which has the additional advantages of improving speed and ... ...

Abstract	Summary: Due to the scale and sparsity of single-cell RNA-sequencing data, traditional plots can obscure vital information. Our R package schex overcomes this by implementing hexagonal binning, which has the additional advantages of improving speed and reducing storage for resulting plots. Availability and implementation: schex is freely available from Bioconductor via http://bioconductor.org/packages/release/bioc/html/schex.html and its development version can be accessed on GitHub via https://github.com/SaskiaFreytag/schex. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Base Sequence ; RNA ; Sequence Analysis, RNA ; Software ; Whole Exome Sequencing
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2019-12-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz907
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Article ; Online: DNA methylation and the preservation of cell identity.

Bogdanović, Ozren / Lister, Ryan

Current opinion in genetics & development

2017 Volume 46, Page(s) 9–14

Abstract: DNA methylation is a major epigenetic modification of vertebrate genomes that is mostly associated with transcriptional repression. During embryogenesis, DNA methylation together with other epigenetic factors plays an essential role in selecting and ... ...

Abstract	DNA methylation is a major epigenetic modification of vertebrate genomes that is mostly associated with transcriptional repression. During embryogenesis, DNA methylation together with other epigenetic factors plays an essential role in selecting and maintaining cell identity. Recent technological advances are now allowing for the exploration of this mark at unprecedented resolution. This has resulted in a wealth of studies describing the developmental roles of DNA methylation in various vertebrate model systems. It is now evident that in certain contexts DNA methylation can act as a key regulator of cell identity establishment, whereas in many other cases the quantity of DNA methylation will merely reflect other upstream regulatory changes. For example, a number of studies have indicated that DNA methylation might be dispensable for pluripotency stages of embryonic development. Nevertheless, targeted deposition and removal of DNA methylation by DNMTs and TET proteins, respectively, appears to be required for vertebrate gastrulation. Here we review the roles of DNA methylation in the establishment and maintenance of cell identity during development, with a special emphasis on insights obtained from in vivo studies.
Language	English
Publishing date	2017-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1077312-5
ISSN	1879-0380 ; 0959-437X
ISSN (online)	1879-0380
ISSN	0959-437X
DOI	10.1016/j.gde.2017.06.007
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