4.8 Article

To the proteome and beyond: advances in single-cell omics profiling for plant systems

Related references

Note: Only part of the references are listed.
Review Plant Sciences

Single-cell analysis of cis-regulatory elements

Alexandre P. Marand et al.

Summary: Plant tissues and organs are composed of different cell types with variations in cell identity and function. Single-cell profiling has emerged as a powerful tool to study the relationship between cellular phenotypic variation and cis-regulatory mechanisms in plants.

CURRENT OPINION IN PLANT BIOLOGY (2022)

Review Spectroscopy

WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT

Teck Yew Low et al.

Summary: Phosphorylation is a crucial form of posttranslational modification for proteins, and phosphoproteomics is the study of phosphorylated proteome using mass spectrometry. This field faces challenges due to the abundant phosphorylated proteins in human proteome. The future of phosphoproteomics involves exploring the noncanonical phosphoproteome and unraveling the dark phosphoproteome.

MASS SPECTROMETRY REVIEWS (2021)

Article Chemistry, Analytical

Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling

Yiran Liang et al.

Summary: Recent advancements in sample preparation and analysis have led to the development of a fully automated platform, autoPOTS, which uses commercially available instrumentation for processing and analyzing low-input and single-cell proteomics samples, making it a convenient option for many laboratories.

ANALYTICAL CHEMISTRY (2021)

Article Cell Biology

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

Xiaosa Xu et al.

Summary: The researchers investigated the transcriptional profiles of 12,525 single cells from developing maize ears, constructing a developmental atlas and validating the results through various methods. They pointed out that these data may facilitate genetic studies by predicting genetic redundancy, integrating transcriptional networks, and identifying candidate genes associated with crop yield traits.

DEVELOPMENTAL CELL (2021)

Article Biochemistry & Molecular Biology

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level

Andrew Farmer et al.

Summary: Plants consist of diverse and specialized cell types, with unique biological functions regulated by cell-type-specific transcriptional programs. Single-nucleus RNA sequencing and single-nucleus assay for transposase accessible chromatin sequencing technologies can establish plant cell-type-specific transcriptomes and uncover additional cell subtypes. The differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.

MOLECULAR PLANT (2021)

Article Biochemistry & Molecular Biology

Transcriptional landscape of rice roots at the single-cell resolution

Qing Liu et al.

Summary: This study analyzed the transcriptomes of rice root tip cells, identifying major cell types and defining novel cell-type-specific marker genes for two cultivars. The research found divergent cell types associated with phytohormone biosynthesis, signaling, and response in rice. Significant differences in cell-type transcript profiles between Arabidopsis and rice were also detected, emphasizing the importance of analyzing tissues across diverse model species.

MOLECULAR PLANT (2021)

Article Biochemical Research Methods

Defining the carrier proteome limit for single-cell proteomics

Tommy K. Cheung et al.

Summary: Single-cell proteomics by mass spectrometry (SCoPE-MS) is a novel method to quantify multiplexed single-cell proteomes, but it faces technical limitations related to isobaric labeling and mass spectrometry. Increasing carrier proteome levels requires a corresponding increase in the number of ions sampled to maintain quantitative accuracy. The introduction of SCPCompanion software assists in rapid evaluation of single-cell proteomic data and recommends parameters for improved data quality.

NATURE METHODS (2021)

Article Biochemical Research Methods

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

Michael J. Taylor et al.

Summary: Biological systems consist of heterogeneous populations of cells that intercommunicate to form functional tissues, with each single cell possessing unique transcriptome, proteome, and metabolome leading to functional differences. Advancements in characterizing omic profiles at a single cell level, including spatially resolved mass spectrometry techniques, have progressed significantly over the past decade.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2021)

Article Multidisciplinary Sciences

Differential biosynthesis and cellular permeability explain longitudinal gibberellin gradients in growing roots

Annalisa Rizza et al.

Summary: The study investigated the distribution of the growth regulatory hormone gibberellin (GA) in plant roots and its impact on cell division and elongation patterns. It found that differentials in biosynthetic enzyme steps and cellular permeability contribute to the endogenous GA gradient, affecting root growth.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemistry & Molecular Biology

A cis-regulatory atlas in maize at single-cell resolution

Alexandre P. Marand et al.

Summary: By analyzing single-cell genomics data from six maize organs, researchers identified cis-regulatory factors and trans-regulatory factors, revealing the crucial role of cell-type-specific regulatory elements in gene expression regulation, and developed the single-cell analysis software Socrates for studying cis-regulatory variation in various species.
Article Cell Biology

Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf

Camila B. Lopez-Anido et al.

Summary: The study investigates the development and regulation of stomatal lineage in Arabidopsis leaf epidermis, revealing detailed cell differentiation processes using single-cell transcriptomics and genetics. It identifies the extended role of transcriptional regulator in reinforcing cell fate commitment through integration of genome-scale datasets and precise functional manipulations.

DEVELOPMENTAL CELL (2021)

Article Biochemical Research Methods

TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing

Jiaming Li et al.

Summary: The development of TMTpro-16plex series expanded the commercial isobaric tagging reagents by nearly 50%, introducing two additional labeling reagents for simultaneous global protein profiling of 18 samples. The analysis of isogenic cell lines' proteome demonstrated that TMTpro-18plex further enhances the sample multiplexing landscape with complex and innovative experimental designs.

JOURNAL OF PROTEOME RESEARCH (2021)

Editorial Material Biochemical Research Methods

Towards resolving proteomes in single cells

Arunima Singh

Summary: The development of methods for single-cell proteomics has led to increased depth and throughput in analysis.

NATURE METHODS (2021)

Article Multidisciplinary Sciences

Quantitative single-cell proteomics as a tool to characterize cellular hierarchies

Erwin M. Schoof et al.

Summary: The study demonstrates a comprehensive experimental and computational workflow that establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses, enabling the exploration of cellular heterogeneity. The approach presented is capable of consistently quantifying around 1000 proteins per cell within limited instrument time.

NATURE COMMUNICATIONS (2021)

Review Biochemistry & Molecular Biology

Space: the final frontier - achieving single-cell, spatially resolved transcriptomics in plants

Sai Guna Ranjan Gurazada et al.

Summary: Single-cell RNA-seq is a high-resolution tool for understanding regulatory networks in biological systems, but its implementation in plants often involves laborious processes. Researchers are working towards improving the 3D spatial transcriptomics resolution in plant tissues, while also seeking opportunities to advance this novel methodology in the plant field.

EMERGING TOPICS IN LIFE SCIENCES (2021)

Article Biochemical Research Methods

Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers

Harrison Specht et al.

Summary: The isobaric carrier approach is widely used in ultrasensitive mass spectrometry analysis of very small samples, balancing peptide sequence identification and protein quantification by optimizing the amount of isobaric carrier and analytical parameters. This method can be applied in various fields, such as single-cell analysis, by adapting experimental designs to different priorities.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2

Harrison Specht et al.

Summary: The SCoPE2 technology was developed to improve the accuracy and throughput of single-cell proteomics through automated sample preparation, revealing the gradual differences in the proteome of macrophages during the enhancement of heterogeneity and allowing differentiation of cell states.

GENOME BIOLOGY (2021)

Article Chemistry, Multidisciplinary

Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell

Yongzheng Cong et al.

Summary: The combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer led to greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions, allowing for more effective MS analysis of multiply charged peptides, resulting in a significantly higher number of protein groups identified from single HeLa cells compared to traditional methods. Differential analysis also showed similar proteome coverage for single microdissected motor neurons and interneurons from human spinal tissue, with the ability to differentiate between the two subpopulations based on label-free quantification.

CHEMICAL SCIENCE (2021)

Article Biochemical Research Methods

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

Vadim Demichev et al.

NATURE METHODS (2020)

Article Biochemical Research Methods

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

Chia-Feng Tsai et al.

MOLECULAR & CELLULAR PROTEOMICS (2020)

Review Biochemical Research Methods

Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies

Liwei Yang et al.

PROTEOMICS (2020)

Article Multidisciplinary Sciences

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics

Yi Yang et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Embracing the dropouts in single-cell RNA-seq analysis

Peng Qiu

NATURE COMMUNICATIONS (2020)

Review Biochemical Research Methods

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

Lindsay K. Pino et al.

MOLECULAR & CELLULAR PROTEOMICS (2020)

Article Multidisciplinary Sciences

Mass-spectrometry-based draft of the Arabidopsis proteome

Julia Mergner et al.

NATURE (2020)

Article Chemistry, Multidisciplinary

Simple Method to Quantify Protein Abundances from 1000 Cells

Burcu Vitrinel et al.

ACS OMEGA (2020)

Article Multidisciplinary Sciences

Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division

Natalie M. Clark et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Biochemical Research Methods

Single-cell Proteomics: Progress and Prospects

Ryan T. Kelly

MOLECULAR & CELLULAR PROTEOMICS (2020)

Article Biochemical Research Methods

diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition

Florian Meier et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Plant stem-cell organization and differentiation at single-cell resolution

James W. Satterlee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

Single-cell protein analysis by mass spectrometry

Nikolai Slavov

CURRENT OPINION IN CHEMICAL BIOLOGY (2020)

Article Plant Sciences

Integrated multi-omics framework of the plant response to jasmonic acid

Mark Zander et al.

NATURE PLANTS (2020)

Article Biochemical Research Methods

DO-MS: Data-Driven Optimization of Mass Spectrometry Methods

R. Gray Huffman et al.

JOURNAL OF PROTEOME RESEARCH (2019)

Review Biochemical Research Methods

Exploiting Interdata Relationships in Next-generation Proteomics Analysis

Burcu Vitrinel et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

Article Biochemistry & Molecular Biology

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

Tian-Qi Zhang et al.

MOLECULAR PLANT (2019)

Review Plant Sciences

Towards Building a Plant Cell Atlas

Seung Y. Rhee et al.

TRENDS IN PLANT SCIENCE (2019)

Review Genetics & Heredity

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

Geng Chen et al.

FRONTIERS IN GENETICS (2019)

Article Chemistry, Analytical

Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis

Anumita Saha-Shah et al.

ANALYTICAL CHEMISTRY (2019)

Review Biochemistry & Molecular Biology

Current best practices in single-cell RNA-seq analysis: a tutorial

Malte D. Luecken et al.

MOLECULAR SYSTEMS BIOLOGY (2019)

Article Biochemical Research Methods

DART-ID increases single-cell proteome coverage

Albert Tian Chen et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Chemistry, Analytical

Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography

Johannes Stadlmann et al.

ANALYTICAL CHEMISTRY (2019)

Article Multidisciplinary Sciences

A systematic evaluation of single cell RNA-seq analysis pipelines

Beate Vieth et al.

NATURE COMMUNICATIONS (2019)

Article Biochemical Research Methods

Characterization of Proteome Variation During Modern Maize Breeding

Lu-Guang Jiang et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

Article Multidisciplinary Sciences

Fungal-induced protein hyperacetylation in maize identified by acetylome profiling

Justin W. Walley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Chemistry, Analytical

Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis

Zi-Yi Li et al.

ANALYTICAL CHEMISTRY (2018)

Article Biochemistry & Molecular Biology

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Daniel D. Seaton et al.

MOLECULAR SYSTEMS BIOLOGY (2018)

Article Multidisciplinary Sciences

Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells

Ying Zhu et al.

NATURE COMMUNICATIONS (2018)

Article Biochemical Research Methods

iDREM: Interactive visualization of dynamic regulatory networks

Jun Ding et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biochemical Research Methods

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Luke Zappia et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biochemical Research Methods

SCENIC: single-cell regulatory network inference and clustering

Sara Aibar et al.

NATURE METHODS (2017)

Review Plant Sciences

Plant Systems Biology at the Single-Cell Level

Marc Libault et al.

TRENDS IN PLANT SCIENCE (2017)

Article Biochemical Research Methods

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

Hirotaka Matsumoto et al.

BIOINFORMATICS (2017)

Article Multidisciplinary Sciences

Integration of omic networks in a developmental atlas of maize

Justin W. Walley et al.

SCIENCE (2016)

Review Plant Sciences

Dynamic Protein Acetylation in Plant-Pathogen Interactions

Gaoyuan Song et al.

FRONTIERS IN PLANT SCIENCE (2016)

Article Plant Sciences

Correlation of mRNA and protein abundance in the developing maize leaf

Lalit Ponnala et al.

PLANT JOURNAL (2014)

Article Biochemical Research Methods

Accounting for technical noise in single-cell RNA-seq experiments

Philip Brennecke et al.

NATURE METHODS (2013)

Review Biochemical Research Methods

Single-cell-type Proteomics: Toward a Holistic Understanding of Plant Function

Shaojun Dai et al.

MOLECULAR & CELLULAR PROTEOMICS (2012)

Article Multidisciplinary Sciences

The protein expression landscape of the Arabidopsis root

Jalean J. Petricka et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Mathematical & Computational Biology

A plausible mechanism for auxin patterning along the developing root

Victoria V. Mironova et al.

BMC SYSTEMS BIOLOGY (2010)

Review Plant Sciences

Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered immunity

Kenichi Tsuda et al.

CURRENT OPINION IN PLANT BIOLOGY (2010)

Review Genetics & Heredity

Plant immunity: towards an integrated view of plant-pathogen interactions

Peter N. Dodds et al.

NATURE REVIEWS GENETICS (2010)

Article Multidisciplinary Sciences

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

Ram Kishor Yadav et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Auxin transport is sufficient to generate a maximum and gradient guiding root growth

Veronica A. Grieneisen et al.

NATURE (2007)

Article Biochemical Research Methods

Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis

Sang-Dong Yoo et al.

NATURE PROTOCOLS (2007)

Article Biochemistry & Molecular Biology

Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis

Mitchell P. Levesque et al.

PLOS BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Mechanisms regulating SHORT-ROOT intercellular movement

KL Gallagher et al.

CURRENT BIOLOGY (2004)