Many needles in a haystack: cell-type specific abiotic stress responses

AbstractRecent advances in genomic technologies have generated large-scale protein-DNA interaction data and open chromatic regions for multiple plant species. To predict condition specific gene regulatory networks using these data, we developed the Condition Specific Regulatory network inference engine (ConSReg), which combines heterogeneous genomic data using sparse linear model followed by feature selection and stability selection to select key regulatory genes. Using Arabidopsis as a model system, we constructed maps of gene regulation under more than 50 experimental conditions including abiotic stresses, cell type-specific expression, and stress responses in individual cell types. Our results show that ConSReg accurately predicted gene expressions (average auROC of 0.84) across multiple testing datasets. We found that, (1) including open chromatin information from ATAC-seq data significantly improves the performance of ConSReg across all tested datasets; (2) choice of negative training samples and length of promoter regions are two key factors that affect model performance. We applied ConSReg to Arabidopsis single cell RNA-seq data of two root cell types (endodermis and cortex) and identified five regulators in two root cell types. Four out of the five regulators have additional experimental evidence to support their roles in regulating gene expression in Arabidopsis roots. By comparing regulatory maps in abiotic stress responses and cell type-specific experiments, we revealed that transcription factors that regulate tissue levels abiotic stresses tend to also regulate stress responses in individual cell types in plants.

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The “Gatekeeper” Concept: Cell-Type Specific Molecular Mechanisms of Plant Adaptation to Abiotic Stress

Molecular Mechanisms in Plant Adaptation ◽

10.1002/9781118860526.ch4 ◽

2015 ◽

pp. 83-115 ◽

Cited By ~ 2

Author(s):

Sam W. Henderson ◽

Matthew Gilliham

Keyword(s):

Abiotic Stress ◽

Molecular Mechanisms ◽

Cell Type ◽

Plant Adaptation ◽

Cell Type Specific

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Versatile Roles of the Receptor-Like Kinase Feronia in Plant Growth, Development and Host-Pathogen Interaction

International Journal of Molecular Sciences ◽

10.3390/ijms21217881 ◽

2020 ◽

Vol 21 (21) ◽

pp. 7881

Author(s):

Dongchao Ji ◽

Tong Chen ◽

Zhanquan Zhang ◽

Boqiang Li ◽

Shiping Tian

Keyword(s):

Stress Responses ◽

Growth And Development ◽

Female Gametophyte ◽

Cell Type ◽

Cellular Processes ◽

Host Pathogen Interaction ◽

Receptor Like Kinase ◽

Ligand Interactions ◽

Cell Type Specific ◽

Growth Development

As a member of the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) protein kinase subfamily, FERONIA (FER) has emerged as a versatile player regulating multifaceted functions in growth and development, as well as responses to environmental factors and pathogens. With the concerted efforts of researchers, the molecular mechanism underlying FER-dependent signaling has been gradually elucidated. A number of cellular processes regulated by FER-ligand interactions have been extensively reported, implying cell type-specific mechanisms for FER. Here, we provide a review on the roles of FER in male-female gametophyte recognition, cell elongation, hormonal signaling, stress responses, responses to fungi and bacteria, and present a brief outlook for future efforts.

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Nuclear dynamics and stress responses in Alzheimer’s disease

Molecular Neurodegeneration ◽

10.1186/s13024-021-00489-6 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Artemis Iatrou ◽

Eric M. Clark ◽

Yanling Wang

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Stress Responses ◽

Cell Type ◽

Nuclear Dynamics ◽

Molecular Changes ◽

Cell Type Specific ◽

Nuclear Alterations ◽

Cellular Stressors ◽

Gene Perturbation

AbstractIn response to extracellular and intracellular stressors, the nucleus and nuclear compartments undergo distinct molecular changes to maintain cell homeostasis. In the context of Alzheimer’s disease, misfolded proteins and various cellular stressors lead to profound structural and molecular changes at the nucleus. This review summarizes recent research on nuclear alterations in AD development, from the nuclear envelope changes to chromatin and epigenetic regulation and then to common nuclear stress responses. Finally, we provide our thoughts on the importance of understanding cell-type-specific changes and identifying upstream causal events in AD pathogenesis and highlight novel sequencing and gene perturbation technologies to address those challenges.

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Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules

10.1101/167932 ◽

2017 ◽

Cited By ~ 1

Author(s):

Kelsey A. Maher ◽

Marko Bajic ◽

Kaisa Kajala ◽

Mauricio Reynoso ◽

Germain Pauluzzi ◽

...

Keyword(s):

Hair Cell ◽

Plant Species ◽

Stress Responses ◽

Binding Sites ◽

Cell Types ◽

Regulatory Elements ◽

Open Chromatin ◽

Cell Type ◽

Cell Type Specific ◽

Accessible Chromatin

ABSTRACTThe transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling of Arabidopsis root hair and non-hair cell types revealed extensive similarity as well as many cell type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell type-specific transcriptomes during development.

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