Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience DOI Creative Commons
Rajiv Kumar Tripathi, Olivia Wilkins

Plant Cell & Environment, Journal Year: 2021, Volume and Issue: 44(7), P. 2006 - 2017

Published: Feb. 2, 2021

Abstract Global warming poses major challenges for plant survival and agricultural productivity. Thus, efforts to enhance stress resilience in plants are key strategies protecting food security. Gene regulatory networks (GRNs) a critical mechanism conferring resilience. Until recently, predicting GRNs of the individual cells that make up other multicellular organisms was impeded by aggregate population scale measurements transcriptome genome‐scale features. With advancement high‐throughput single cell RNA‐seq assays, learning is now possible, principle. In this article, we report on recent advances experimental analytical methodologies sequencing assays especially as they have been applied study plants. We highlight ongoing scGRN prediction, finally, opportunity use discovery studying ultimately enhancing abiotic

Language: Английский

A cis-regulatory atlas in maize at single-cell resolution DOI Creative Commons
Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti

et al.

Cell, Journal Year: 2021, Volume and Issue: 184(11), P. 3041 - 3055.e21

Published: May 1, 2021

Language: Английский

Citations

268
A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants DOI Creative Commons
Rachel Shahan, Che‐Wei Hsu, Trevor M. Nolan

et al.

Developmental Cell, Journal Year: 2022, Volume and Issue: 57(4), P. 543 - 560.e9

Published: Feb. 1, 2022

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal signatures underlying developmental trajectories. To map gene expression dynamics across root cell types time, we built a comprehensive, organ-scale atlas at single-cell resolution. addition to estimating progressions in pseudotime, employed mathematical concept of optimal transport infer trajectories identify their regulators. demonstrate utility interpret new datasets, profiled mutants two key regulators resolution, shortroot scarecrow. We report transcriptomic vivo evidence tissue trans-differentiation mixed identity phenotype Our results support as rich community resource unraveling programs that specify maintain regulate

Language: Английский

Citations

242
Cis-regulatory sequences in plants: Their importance, discovery, and future challenges DOI Creative Commons
Robert J. Schmitz, Erich Grotewold, Maike Stam

et al.

The Plant Cell, Journal Year: 2021, Volume and Issue: 34(2), P. 718 - 741

Published: Nov. 18, 2021

The identification and characterization of cis-regulatory DNA sequences how they function to coordinate responses developmental environmental cues is paramount importance plant biology. Key these regulatory processes are modules (CRMs), which include enhancers silencers. Despite the extraordinary advances in high-quality sequence assemblies genome annotations, understanding CRMs, regulate gene expression, lag significantly behind. This especially true for their distinguishing characteristics activity states. Here, we review current knowledge on CRMs breakthrough technologies enabling identification, characterization, validation CRMs; compare genomic distributions with respect target genes between different species, discuss role transposable elements harboring evolution expression. an exciting time study cis-regulomes plants; however, significant existing challenges need be overcome fully understand appreciate biology crop improvement.

Language: Английский

Citations

235
Single-Cell Transcriptome Analysis in Plants: Advances and Challenges DOI Creative Commons
Rahul Shaw, Xin Tian, Jian Xu

et al.

Molecular Plant, Journal Year: 2020, Volume and Issue: 14(1), P. 115 - 126

Published: Nov. 2, 2020

Language: Английский

Citations

201
Advances and Opportunities in Single-Cell Transcriptomics for Plant Research DOI Open Access
Carolin Seyfferth, Jim Renema, Jos R. Wendrich

et al.

Annual Review of Plant Biology, Journal Year: 2021, Volume and Issue: 72(1), P. 847 - 866

Published: March 17, 2021

Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of analyses to level individual cell. The field plant biology has fully embraced single-cell transcriptomics and is rapidly expanding portfolio available technologies applications. In this review, we give an overview main advances in over past few years provide reader with accessible guideline covering all steps, from sample preparation data analysis. We end offering a glimpse how these will shape accelerate plant-specific research near future.

Language: Английский

Citations

159
Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters DOI
Tobias Jores, Jackson Tonnies, Travis Wrightsman

et al.

Nature Plants, Journal Year: 2021, Volume and Issue: 7(6), P. 842 - 855

Published: June 3, 2021

Language: Английский

Citations

136
cis-Regulatory Elements in Plant Development, Adaptation, and Evolution DOI Creative Commons
Alexandre P. Marand, Andrea L. Eveland, Kerstin Kaufmann

et al.

Annual Review of Plant Biology, Journal Year: 2023, Volume and Issue: 74(1), P. 111 - 137

Published: Jan. 6, 2023

Regulatory elements encode the genomic blueprints that ensure proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to environment. Accumulating evidence implicates changes as a major source phenotypic novelty in eukaryotes, including acute phenotypes such disease cancer mammals. Moreover, genetic epigenetic variation affecting

Language: Английский

Citations

130
Machine learning bridges omics sciences and plant breeding DOI
Jun Yan, Xiangfeng Wang

Trends in Plant Science, Journal Year: 2022, Volume and Issue: 28(2), P. 199 - 210

Published: Sept. 21, 2022

Language: Английский

Citations

76
Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii DOI Creative Commons
Yue Sun,

Yifei Han,

Kuang Sheng

et al.

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(4), P. 694 - 708

Published: Feb. 10, 2023

Comprehensive utilization of cottonseeds is limited by the presence pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, trait found in only few Australian wild species, including Gossypium bickii. Introgression this into cultivated species proved to be difficult. Understanding biological processes toward gland morphogenesis associated underlying molecular mechanisms will facilitate breeding varieties with plant. In study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons germinating G. bickii 48 h after imbibition. Clustered 14 distinct clusters unsupervisedly, these cells could grouped eight cell populations assistance known marker genes. were well separated others parenchyma cells, secretory apoptotic cells. By integrating developmental trajectory, transcription factor regulatory networks, core functional validation, we established model for formation. model, light gibberellin verified promote formation glands. addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), affect Collectively, findings provide new insights lay cornerstone future scRNA-seq investigations.

Language: Английский

Citations

43
Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis DOI Creative Commons
Michael Borg, Ranjith K. Papareddy, Rodolphe Dombey

et al.

eLife, Journal Year: 2021, Volume and Issue: 10

Published: Jan. 25, 2021

Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant algal cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore dynamic relationship chromatin accessibility epigenetic modifications during form in Arabidopsis. The diploid-to-haploid transition governed by loss H3K9me2 DNA demethylation transposon-associated cis -regulatory elements. This event associated with dramatic changes transcriptional reprogramming. In contrast, global H3K27me3 shapes landscape poised to re-initiate back after fertilisation. Hence, reprogramming events rewire transcription through major reorganisation regulatory epigenome guide alternation generations flowering plants.

Language: Английский

Citations

85