共 48 条
Single-cell analysis opens a goldmine for plant functional studies
被引:12
作者:

Xu, Xiaosa
论文数: 0 引用数: 0
h-index: 0
机构:
Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

Jackson, David
论文数: 0 引用数: 0
h-index: 0
机构:
Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
机构:
[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
基金:
美国国家科学基金会;
关键词:
STOMATAL LINEAGE;
GENE-EXPRESSION;
MAIZE;
MAP;
DIFFERENTIATION;
TRAJECTORIES;
RESOLUTION;
LANDSCAPE;
ATLAS;
D O I:
10.1016/j.copbio.2022.102858
中图分类号:
Q5 [生物化学];
学科分类号:
071010 ;
081704 ;
摘要:
Functional studies in biology require the identification of genes, regulatory elements, and networks, followed by a deep understanding of how they orchestrate to specify cell types, mediate signaling, and respond to internal and external cues over evolutionary timescales. Advances in single-cell analysis have enabled biologists to tackle these questions at the resolution of the individual cell. Here, we highlight recent studies in plants that have embraced single-cell analyses to facilitate functional studies. This review will provide guidance and perspectives for incorporating these advanced approaches in plant research for the coming decades.
引用
收藏
页数:8
相关论文
共 48 条
[1]
A gene expression map of the Arabidopsis root
[J].
Birnbaum, K
;
Shasha, DE
;
Wang, JY
;
Jung, JW
;
Lambert, GM
;
Galbraith, DW
;
Benfey, PN
.
SCIENCE,
2003, 302 (5652)
:1956-1960

Birnbaum, K
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Shasha, DE
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Wang, JY
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Jung, JW
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Lambert, GM
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Galbraith, DW
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Benfey, PN
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA
[2]
A high-resolution root spatiotemporal map reveals dominant expression patterns
[J].
Brady, Siobhan M.
;
Orlando, David A.
;
Lee, Ji-Young
;
Wang, Jean Y.
;
Koch, Jeremy
;
Dinneny, Jose R.
;
Mace, Daniel
;
Ohler, Uwe
;
Benfey, Philip N.
.
SCIENCE,
2007, 318 (5851)
:801-806

Brady, Siobhan M.
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Orlando, David A.
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Lee, Ji-Young
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Wang, Jean Y.
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Koch, Jeremy
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Dinneny, Jose R.
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Mace, Daniel
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Ohler, Uwe
论文数: 0 引用数: 0
h-index: 0
机构: Duke Univ, Dept Biol, Durham, NC 27708 USA

Benfey, Philip N.
论文数: 0 引用数: 0
h-index: 0
机构:
Duke Univ, Dept Biol, Durham, NC 27708 USA Duke Univ, Dept Biol, Durham, NC 27708 USA
[3]
Single-cell genomics in plants: current state, future directions, and hurdles to overcome
[J].
Cuperus, Josh T.
.
PLANT PHYSIOLOGY,
2022, 188 (02)
:749-755

Cuperus, Josh T.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA
[4]
The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana
[J].
Deal, Roger B.
;
Henikoff, Steven
.
NATURE PROTOCOLS,
2011, 6 (01)
:56-68

Deal, Roger B.
论文数: 0 引用数: 0
h-index: 0
机构:
Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98104 USA Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98104 USA

Henikoff, Steven
论文数: 0 引用数: 0
h-index: 0
机构:
Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98104 USA
Howard Hughes Med Inst, Seattle, WA USA Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98104 USA
[5]
Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing
[J].
Denyer, Tom
;
Ma, Xiaoli
;
Klesen, Simon
;
Scacchi, Emanuele
;
Nieselt, Kay
;
Timmermans, Marja C. P.
.
DEVELOPMENTAL CELL,
2019, 48 (06)
:840-+

Denyer, Tom
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany

Ma, Xiaoli
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany

Klesen, Simon
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany

Scacchi, Emanuele
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany

Nieselt, Kay
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Bioinformat, Sand 14, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany

Timmermans, Marja C. P.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany
[6]
Crafting a blueprint for single-cell RNA sequencing
[J].
Denyer, Tom
;
Timmermans, Marja C. P.
.
TRENDS IN PLANT SCIENCE,
2022, 27 (01)
:92-103

Denyer, Tom
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany

Timmermans, Marja C. P.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany Univ Tubingen, Ctr Plant Mol Biol, Morgenstelle 32, D-72076 Tubingen, Germany
[7]
The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution
[J].
Dorrity, Michael W.
;
Alexandre, Cristina M.
;
Hamm, Morgan O.
;
Vigil, Anna-Lena
;
Fields, Stanley
;
Queitsch, Christine
;
Cuperus, Josh T.
.
NATURE COMMUNICATIONS,
2021, 12 (01)

Dorrity, Michael W.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

Alexandre, Cristina M.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

Hamm, Morgan O.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

Vigil, Anna-Lena
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Nevada, Sch Life Sci, Las Vegas, NV 89154 USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

Fields, Stanley
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA
Univ Washington, Dept Med, Seattle, WA USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

Queitsch, Christine
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

Cuperus, Josh T.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA
[8]
Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level
[J].
Farmer, Andrew
;
Thibivilliers, Sandra
;
Ryu, Kook Hui
;
Schiefelbein, John
;
Libault, Marc
.
MOLECULAR PLANT,
2021, 14 (03)
:372-383

Farmer, Andrew
论文数: 0 引用数: 0
h-index: 0
机构:
Natl Ctr Genome Resources, Santa Fe, NM 87505 USA Natl Ctr Genome Resources, Santa Fe, NM 87505 USA

Thibivilliers, Sandra
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Nebraska, Ctr Plant Sci Innovat, Beadle Ctr, Dept Agron & Hort, Lincoln, NE 68503 USA Natl Ctr Genome Resources, Santa Fe, NM 87505 USA

论文数: 引用数:
h-index:
机构:

论文数: 引用数:
h-index:
机构:

Libault, Marc
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Nebraska, Ctr Plant Sci Innovat, Beadle Ctr, Dept Agron & Hort, Lincoln, NE 68503 USA Natl Ctr Genome Resources, Santa Fe, NM 87505 USA
[9]
MINI-EX:Integrative inference of single-cell gene regulatory networks in plants
[J].
Ferrari, Camilla
;
Perez, Nicolas Manosalva
;
Vandepoele, Klaas
.
MOLECULAR PLANT,
2022, 15 (11)
:1807-1824

Ferrari, Camilla
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium
VIB, Ctr Plant Syst Biol, B-9052 Ghent, Belgium Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

Perez, Nicolas Manosalva
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium
VIB, Ctr Plant Syst Biol, B-9052 Ghent, Belgium Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

Vandepoele, Klaas
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium
VIB, Ctr Plant Syst Biol, B-9052 Ghent, Belgium
Univ Ghent, Bioinformat Inst Ghent, B-9052 Ghent, Belgium Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium
[10]
A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana
[J].
Gala, Hardik P.
;
Lanctot, Amy
;
Jean-Baptiste, Ken
;
Guiziou, Sarah
;
Chu, Jonah C.
;
Zemke, Joseph E.
;
George, Wesley
;
Queitsch, Christine
;
Cuperus, Josh T.
;
Nemhauser, Jennifer L.
.
PLANT CELL,
2021, 33 (07)
:2197-2220

Gala, Hardik P.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Biol, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

论文数: 引用数:
h-index:
机构:

Jean-Baptiste, Ken
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

Guiziou, Sarah
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Biol, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

Chu, Jonah C.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Biol, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

Zemke, Joseph E.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Biol, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

George, Wesley
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Biol, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

Queitsch, Christine
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

Cuperus, Josh T.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA

Nemhauser, Jennifer L.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Washington, Dept Biol, Seattle, WA 98195 USA Univ Washington, Dept Biol, Seattle, WA 98195 USA