Thomas Eekhout
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View article: Conserved transcriptional reprogramming in nematode infected root cells
Conserved transcriptional reprogramming in nematode infected root cells Open
Plant-parasitic nematodes are responsible for important annual losses in crop productivity worldwide 1,2 . Although the formation of feeding organs within the roots is essential for successful sedentary parasitism 3 , the molecular mechani…
View article: Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics
Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics Open
Summary Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step toward engineering improved drought resilience. However, t…
View article: Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing
Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing Open
Motivation Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes. Results We introduce scywalker, an innovative and scalable package developed to comprehensively analyze long-read sequen…
View article: Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics
Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics Open
Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step towards engineering improved drought resilience. However, the mole…
View article: The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth
The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth Open
During the process of secondary growth, the vascular cambium produces the conductive xylem and phloem cells, while the phellogen (cork cambium) deposit phellem (cork) as the outermost protective barrier. Although most of the secondary tiss…
View article: The stem cell niche transcription factor <i>ETHYLENE RESPONSE FACTOR 115</i> participates in aluminum‐induced terminal differentiation in Arabidopsis roots
The stem cell niche transcription factor <i>ETHYLENE RESPONSE FACTOR 115</i> participates in aluminum‐induced terminal differentiation in Arabidopsis roots Open
Aluminum‐dependent stoppage of root growth requires the DNA damage response (DDR) pathway including the p53‐like transcription factor SUPPRESSOR OF GAMMA RADIATION 1 (SOG1), which promotes terminal differentiation of the root tip in respon…
View article: Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing
Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing Open
We introduce scywalker , an innovative and scalable package developed to comprehensively analyze long-read nanopore sequencing data of full-length single-cell or single-nuclei cDNA. Existing nanopore single-cell data analysis tools showed …
View article: Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics
Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics Open
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidatin…
View article: Cell type–specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division
Cell type–specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division Open
In Arabidopsis thaliana, brassinosteroid (BR) signaling and stomatal development are connected through the SHAGGY/GSK3-like kinase BR INSENSITIVE2 (BIN2). BIN2 is a key negative regulator of BR signaling but it plays a dual role in stomata…
View article: PAT1-type GRAS-domain proteins control regeneration by activating DOF3.4 to drive cell proliferation in Arabidopsis roots
PAT1-type GRAS-domain proteins control regeneration by activating DOF3.4 to drive cell proliferation in Arabidopsis roots Open
Plant roots possess remarkable regenerative potential owing to their ability to replenish damaged or lost stem cells. ETHYLENE RESPONSE FACTOR 115 (ERF115), one of the key molecular elements linked to this potential, plays a predominant ro…
View article: Distinctive and complementary roles of E2F transcription factors during plant replication stress responses
Distinctive and complementary roles of E2F transcription factors during plant replication stress responses Open
Survival of living organisms is fully dependent on their maintenance of genome integrity, being permanently threatened by replication stress in proliferating cells. Although the plant DNA damage response (DDR) regulator SOG1 has been demon…
View article: Cell type-specific attenuation of brassinosteroid signalling drives stomatal asymmetric cell division
Cell type-specific attenuation of brassinosteroid signalling drives stomatal asymmetric cell division Open
In Arabidopsis thaliana , the negative brassinosteroid (BR) signalling regulator, BR INSENSITIVE2 (BIN2) promotes and restricts stomatal asymmetric cell division (ACD) depending on its subcellular localization, which is regulated by the st…
View article: Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division
Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division Open
The anaphase-promoting complex/cyclosome (APC/C) marks key cell cycle proteins for proteasomal breakdown, thereby ensuring unidirectional progression through the cell cycle. Its target recognition is temporally regulated by activating subu…
View article: The APC/C<sup>CCS52A2</sup> E3-Ligase Complex targeted PKN1 Protein is a Plant Lineage-Specific Driver of Cell Division
The APC/C<sup>CCS52A2</sup> E3-Ligase Complex targeted PKN1 Protein is a Plant Lineage-Specific Driver of Cell Division Open
The anaphase-promoting complex/cyclosome (APC/C) marks key cell cycle proteins for proteasomal breakdown, thereby ensuring unidirectional progression through the cell cycle. Its target recognition is temporally regulated by activating subu…
View article: A Mutation in DNA Polymerase α Rescues WEE1KO Sensitivity to HU
A Mutation in DNA Polymerase α Rescues WEE1KO Sensitivity to HU Open
During DNA replication, the WEE1 kinase is responsible for safeguarding genomic integrity by phosphorylating and thus inhibiting cyclin-dependent kinases (CDKs), which are the driving force of the cell cycle. Consequentially, wee1 mutant p…
View article: Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death
Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death Open
The ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR) kinases coordinate the DNA damage response. The roles described for Arabidopsis thaliana ATR and ATM are assumed to be conserved over other plant species, but molecular…
View article: G2/M-checkpoint activation in <i>fasciata1</i> rescues an aberrant S-phase checkpoint but causes genome instability
G2/M-checkpoint activation in <i>fasciata1</i> rescues an aberrant S-phase checkpoint but causes genome instability Open
The WEE1 and ATM AND RAD3-RELATED (ATR) kinases are important regulators of the plant intra-S-phase checkpoint; consequently, WEE1KO and ATRKO roots are hypersensitive to replication-inhibitory drugs. Here, we report on a loss-of-function …
View article: A morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root
A morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root Open
The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but did not identify a simple consistent positive or negative impact on a basic cellular parameter that would comprehensively ex…
View article: Advances and Opportunities in Single-Cell Transcriptomics for Plant Research
Advances and Opportunities in Single-Cell Transcriptomics for Plant Research Open
Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcrip…
View article: Loss of FAS1 function reveals rescue of an aberrant intra-S-phase checkpoint by the G2/M checkpoint regulator SOG1<sup>1[OPEN]</sup>
Loss of FAS1 function reveals rescue of an aberrant intra-S-phase checkpoint by the G2/M checkpoint regulator SOG1<sup>1[OPEN]</sup> Open
The WEE1 and ATR kinases represent important regulators of the plant intra-S-phase checkpoint, as evidenced by the hypersensitivity of WEE1 KO and ATR KO roots to replication inhibitory drugs. Here, we report on the identification of a def…
View article: Arabidopsis casein kinase 2 triggers stem cell exhaustion under Al toxicity and phosphate deficiency through activating the DNA damage response pathway
Arabidopsis casein kinase 2 triggers stem cell exhaustion under Al toxicity and phosphate deficiency through activating the DNA damage response pathway Open
Aluminum (Al) toxicity and inorganic phosphate (Pi) limitation are widespread chronic abiotic and mutually enhancing stresses that profoundly affect crop yield. Both stresses strongly inhibit root growth, resulting from a progressive exhau…
View article: Arabidopsis Casein Kinase 2 triggers Stem Cell Exhaustion under Al Toxicity and Phosphate Deficiency Through activation of the DNA Damage Response pathway
Arabidopsis Casein Kinase 2 triggers Stem Cell Exhaustion under Al Toxicity and Phosphate Deficiency Through activation of the DNA Damage Response pathway Open
Aluminum (Al) toxicity and inorganic phosphate (Pi) limitation are widespread chronic abiotic and mutually enhancing stresses that profoundly affect crop yield. Both stresses cause a strong inhibition of root growth, resulting from a progr…
View article: The Cyclin CYCA3;4 Is a Postprophase Target of the APC/C <sup>CCS52A2</sup> E3-Ligase Controlling Formative Cell Divisions in Arabidopsis
The Cyclin CYCA3;4 Is a Postprophase Target of the APC/C <sup>CCS52A2</sup> E3-Ligase Controlling Formative Cell Divisions in Arabidopsis Open
The anaphase promoting complex/cyclosome (APC/C) controls unidirectional progression through the cell cycle by marking key cell cycle proteins for proteasomal turnover. Its activity is temporally regulated by the docking of different activ…
View article: Rocks in the auxin stream: Wound-induced auxin accumulation and <i>ERF115</i> expression synergistically drive stem cell regeneration
Rocks in the auxin stream: Wound-induced auxin accumulation and <i>ERF115</i> expression synergistically drive stem cell regeneration Open
Significance Plants show remarkable regenerative abilities, allowing them to recover from wounds and organ loss. This regenerative capacity is controlled in part by auxin, the most promiscuous plant hormone controlling organogenesis and ti…