Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation

Drapek, Colleen; Sparks, Erin E.; Benfey, Philip N.

doi:10.1016/j.tig.2017.05.002

Cited by 44 publications

(35 citation statements)

References 67 publications

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“…To test the quality of the atlas annotation, we used Seurat to perform differential gene expression analyses and asked if expected markers are enriched in each of the twelve cell type groups produced with our method as compared to the atlas as a whole. We observed enrichment of known cell type markers in their expected cell type groups 12 (Fig 1d) and also identified many new genes that are enriched in a cell type or developmental stage (Supplementary Dataset 6). We subsequently asked if genes with cell-type specific expression patterns also show localized expression along the developmental gradient.…”

Section: Cell Annotation Places Tissues In Known Developmental Contextsmentioning

confidence: 82%

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

Shahan

Hsu

Nolan

et al. 2020

Preprint

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SummaryCell fate acquisition is a fundamental developmental process in all multicellular organisms. Yet, much is unknown regarding how a cell traverses the pathway from stem cell to terminal differentiation. Advances in single cell genomics1 hold promise for unraveling developmental mechanisms2–3 in tissues4, organs5–6, and organisms7–8. However, lineage tracing can be challenging for some tissues9 and integration of high-quality datasets is often necessary to detect rare cell populations and developmental states10,11. Here, we harmonized single cell mRNA sequencing data from over 110,000 cells to construct a comprehensive atlas for a stereotypically developing organ with indeterminate growth, the Arabidopsis root. To test the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single cell resolution, shortroot and scarecrow. Although both transcription factors are required for early specification of cell identity12, our results suggest the existence of an alternative pathway acting in mature cells to specify endodermal identity, for which SHORTROOT is required. Uncovering the architecture of this pathway will provide insight into specification and stabilization of the endodermis, a tissue analogous to the mammalian epithelium. Thus, the atlas is a pivotal advance for unraveling the transcriptional programs that specify and maintain cell identity to regulate organ development in space and time.

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Section: Cell Annotation Places Tissues In Known Developmental Contextsmentioning

confidence: 82%

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

Shahan

Hsu

Nolan

et al. 2020

Preprint

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“…In general, the answer involves a complex interplay between signals and gene regulation. This is true both during development of multicellular eukaryotes (Davidson and Levine, ; Frum and Ralston, ; Drapek et al , ) and during transitions in microbial communities that lead to different cell types (Bush et al , ; van Gestel et al , ; Norman et al , ; Kroos, ). Bacterial cells in microbial communities adopt different fates as gene regulatory networks (GRNs) respond to a variety of signals, including some generated by other cells.…”

Section: Introductionmentioning

confidence: 99%

Systematic analysis of the Myxococcus xanthus developmental gene regulatory network supports posttranslational regulation of FruA by C‐signaling

Saha

Patra

Igoshin

et al. 2019

Molecular Microbiology

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Upon starvation Myxococcus xanthus undergoes multicellular development. Rod-shaped cells move into mounds in which some cells differentiate into spores. Cells begin committing to sporulation at 24-30 h poststarvation, but the mechanisms governing commitment are unknown. FruA and MrpC are transcription factors that are necessary for commitment. They bind cooperatively to promoter regions and activate developmental gene transcription, including that of the dev operon. Leading up to and during the commitment period, dev mRNA increased in wild type, but not in a mutant defective in C-signaling, a short-range signaling interaction between cells that is also necessary for commitment. The C-signaling mutant exhibited ~20-fold less dev mRNA than wild type at 30 h poststarvation, despite a similar level of MrpC and only 2-fold less FruA. Boosting the FruA level twofold in the C-signaling mutant had little effect on the dev mRNA level, and dev mRNA was not less stable in the C-signaling mutant. Neither did high cooperativity of MrpC and FruA binding upstream of the dev promoter explain the data. Rather, our systematic experimental and computational analyses support a model in which C-signaling activates FruA at least ninefold posttranslationally in order to commit a cell to spore formation.

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“…They act in combination to form genetic regulatory circuits involved in transcriptional control (Megraw et al, 2016;Cora et al, 2017). A significant body of research is dedicated to understanding how transcription factors are involved in the regulation of multiple cellular processes in Arabidopsis thaliana, one of the best studied plant model systems (Taylor-Teeples et al, 2015;González-Morales et al, 2016;Drapek et al, 2017). In contrast, broad scale studies of sRNAmediated regulation in A. thaliana are not common and their scope is limited due to challenges posed by the high false positive rate of bioinformatic predictions of small RNA activities (Ding et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs

Vargas-Asencio

Perry

2020

Front. Plant Sci.

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Gene regulation involves the orchestrated action of multiple regulators to fine-tune the expression of genes. Hierarchical interactions and co-regulation among regulators are commonly observed in biological systems, leading to complex regulatory networks. Small RNA (sRNAs) have been shown to be important regulators of gene expression due to their involvement in multiple cellular processes. In plants, microRNA (miRNAs) and phased small interfering RNAs (phasiRNAs) correspond to two well-characterized types of sRNAs involved in the regulation of posttranscriptional gene expression, although information about their targets and interactions with other gene expression regulators is limited. We describe an extended sRNA-mediated regulatory network in Arabidopsis thaliana that provides a reference frame to understand sRNA biogenesis and activity at the genomewide level. This regulatory network combines a comprehensive evaluation of phasiRNA production and sRNA targets supported by degradome data. The network includes 17% of genes in the A. thaliana genome, representing~50% annotated gene ontology (GO) functional categories. Approximately 14% of genes with GO annotations corresponding to regulation of gene expression were found to be under sRNA control. The unbiased bioinformatic approach used to produce the network was able to detect 107 PHAS loci (regions of phasiRNA production), 5,047 active phasiRNAs (~70% of which were non-canonical), and reconstruct 17 regulatory modules resulting from complex regulatory interactions between different sRNA-regulatory pathways. Known regulatory modules like miR173-TAS-PPR/TPR and miR390-TAS3-ARF/F-box were faithfully reconstructed and expanded, illustrating the accuracy and sensitivity of the methods and providing confidence for the validity of findings of previously unrecognized modules. The network presented here includes a 2X increase in the number of identified PHAS loci, a large complement (~70%) of non-canonical phasiRNAs, and the most comprehensive

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Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation

Cited by 44 publications

References 67 publications

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

A single cellArabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants

Systematic analysis of the Myxococcus xanthus developmental gene regulatory network supports posttranslational regulation of FruA by C‐signaling

A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs

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