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| Status |
Public on Sep 30, 2020 |
| Title |
A cis-regulatory atlas of maize single cells |
| Organisms |
Arabidopsis thaliana; Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Cis-regulatory elements (CREs) encode the genomic blueprints for coordinating the spatiotemporal regulation of gene transcription programs necessary for highly specialized cellular functions. To identify cis-regulatory elements underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in an atlas of Zea mays tissues and organs. We describe 92 distinct patterns of chromatin accessibility across more than 165,913 putative CREs, greater than 56,575 cells, and 52 known cell-types using a novel regularized quasibinomial logistic model for estimating single cell accessibility. Cell-type specification could be largely explained by combinatorial accessibility of transcription factors (TFs) and their associated binding. Analysis of cell type-specific co-accessible chromatin recapitulated higher-order chromatin interactions, providing novel insight into cell type-specific regulatory dynamics. Integration of genetic diversity data revealed cell-type specific CREs contributed to specific morphological and molecular phenotypic traits indicative of their cellular functions, expanding our understanding of the molecular influence of complex traits in a eukaryotic species.
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| Overall design |
All samples were integrated into a single all vs. all analysis. Several organs (leaf, axillary buds, embyonic roots, crown roots) were profiled with biological replicates.
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| Contributor(s) |
Schmitz RJ, Marand AP |
| Citation(s) |
33964211 |
| |
| Submission date |
Jul 27, 2020 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Street address |
B416 Davison Life Sciences
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA648930 |
| SRA |
SRP273727 |
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