Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks at a cell-type specific manner. Here we presented a reference single-cell transcriptomic atlas of Arabidopsis seedlings...

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Bibliographic Details
Published in:bioRxiv
Main Authors: Cao, Shanni, He, Chao, Zhao, Xue, Yu, Ranran, Li, Yuqi, Fang, Wen, Chen-Yu, Zhang, Yan, Wenhao, Chen, Dijun
Format: Paper
Language:English
Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 25.10.2022
Cold Spring Harbor Laboratory
Edition:1.1
Subjects:
Bioinformatics
Cell fate
Gene expression
Gene regulation
Integration
Morphogenesis
Seedlings
Transcription factors
Transcriptomics
ISSN:2692-8205, 2692-8205
Online Access:Get full text
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Summary:Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks at a cell-type specific manner. Here we presented a reference single-cell transcriptomic atlas of Arabidopsis seedlings by integration of 40 published scRNA-seq datasets from representative tissues as well as the entire under- and above-ground parts. We identified 34 distinct cell types or states, largely expanding our current view of plant cell compositions. We then mapped the developmental trajectory of root-shoot lineage separation and identified differential gene expression programs that may regulate the cell fate determination of under- and above-ground organs. Lastly, we systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordination manner to control cell-type specific gene expression. Taken together, our study not only offers a valuable resource plant cell atlas exploration but also provides molecular insights into gene-regulatory programs that determines organ specify, particularly the differentiation between root and shoot.
Bibliography:SourceType-Working Papers-1
ObjectType-Working Paper/Pre-Print-1
content type line 50
ISSN:2692-8205
2692-8205
DOI:10.1101/2022.10.24.513543