Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression

The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24h rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant circadian clock and suggest that unlike the centralised mammalian clock, the clock has multiple points of coordination in Arabidopsis.

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Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression

eLife ◽

10.7554/elife.31700 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 32

Author(s):

Peter D Gould ◽

Mirela Domijan ◽

Mark Greenwood ◽

Isao T Tokuda ◽

Hannah Rees ◽

...

Keyword(s):

Gene Expression ◽

Circadian Clock ◽

Single Cell ◽

Feedback Loop ◽

Root Tip ◽

Single Cell Level ◽

Cell Coupling ◽

Cell Level ◽

Spatial Waves ◽

Plant Clock

The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24-hr rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days under constant environmental conditions. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant clock and suggest that unlike the centralised mammalian clock, the Arabidopsis clock has multiple coordination points.

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Faculty Opinions recommendation of Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733113604.793569737 ◽

2020 ◽

Author(s):

Alex Webb

Keyword(s):

Gene Expression ◽

Circadian Clock ◽

Single Cell ◽

Spatial Waves

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Gene expression profiling of the different stages of Arabidopsis thaliana trichome development on the single cell level

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2007.11.001 ◽

2008 ◽

Vol 46 (2) ◽

pp. 160-173 ◽

Cited By ~ 26

Author(s):

Sergiy Kryvych ◽

Victoria Nikiforova ◽

Michel Herzog ◽

Daniel Perazza ◽

Joachim Fisahn

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Single Cell ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Single Cell Level ◽

Cell Level ◽

Trichome Development

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Unmasking cellular response of a bloom-forming alga to virus infection by resolving expression profiling at a single-cell level

10.1101/186981 ◽

2017 ◽

Author(s):

Shilo Rosenwasser ◽

Miguel J. Frada ◽

David Pilzer ◽

Ron Rotkopf ◽

Assaf Vardi

Keyword(s):

Gene Expression ◽

Viral Infection ◽

Single Cell ◽

Host Defense ◽

Host Response ◽

Expression Profiles ◽

Life Cycles ◽

Viral Gene ◽

Single Cell Level ◽

Cell Level

AbstractMarine viruses are major evolutionary and biogeochemical drivers of microbial life in the ocean. Host response to viral infection typically includes virus-induced rewiring of metabolic network to supply essential building blocks for viral assembly, as opposed to activation of anti-viral host defense. Nevertheless, there is a major bottleneck to accurately discern between viral hijacking strategies and host defense responses when averaging bulk population response. Here we use Emiliania huxleyi, a bloom-forming alga and its specific virus (EhV), as one of the most ecologically important host-virus model system in the ocean. Using automatic microfluidic setup to capture individual algal cells, we quantified host and virus gene expression on a single-cell resolution during the course of infection. We revealed high heterogeneity in viral gene expression among individual cells. Simultaneous measurements of expression profiles of host and virus genes at a single-cell level allowed mapping of infected cells into newly defined infection states and uncover a yet unrecognized early phase in host response that occurs prior to viral expression. Intriguingly, resistant cells emerged during viral infection, showed unique expression profiles of metabolic genes which can provide the basis for discerning between viral resistant and sensitive cells within heterogeneous populations in the marine environment. We propose that resolving host-virus arms race at a single-cell level will provide important mechanistic insights into viral life cycles and will uncover host defense strategies.

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Circulating melanoma cells isolated from clinical blood samples and characterized by full-length mRNA sequencing at single-cell level.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.10539 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. 10539-10539 ◽

Cited By ~ 1

Author(s):

Yu-Chieh Wang ◽

Daniel Ramskold ◽

Shujun Luo ◽

Robin Li ◽

Qiaolin Deng ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Expression Patterns ◽

Melanoma Cells ◽

Clinical Samples ◽

Single Cell Level ◽

Cell Level ◽

Blood Samples

10539 Background: Melanoma is the most aggressive type of skin cancer. Late-stage melanoma is highly metastatic and currently lacks effective treatment. This discouraging clinical observation highlights the need for a better understanding of the molecular mechanisms underlying melanoma initiation and progression and for developing new therapeutic approaches based on novel targets. Although genome-wide transcriptome analyses have been frequently used to study molecular alterations in clinical samples, it has been technically challenging to obtain the transcriptomic profiles at single-cell level. Methods: Using antibody-mediated magnetic activated cell separation (MACS), we isolated and individualized putative circulating melanoma cells (CMCs) from the blood samples of the melanoma patients at advance stages. The transcriptomic analysis based on a novel and robust mRNA-Seq protocol (Smart-Seq) was established and applied to the putative CMCs for single-cell profiling. Results: We have discovered distinct gene expression patterns, including new putative markers for CMCs. Meanwhile, the gene expression profiles derived of the CMC candidates isolated from the patient’s blood samples are closely-related to the expression profiles of other cells originated from human melanocytes, including normal melanocytes in primary culture and melanoma cell lines. Compared with existing methods, Smart-Seq has improved read coverage across transcripts, which provides advantage for better analyzing transcript isoforms and SNPs. Conclusions: Our results suggest that the techniques developed in this research for cell isolation and transcriptomic analyses can potentially be used for addressing many biological and clinical questions requiring genomewide transcriptome profiling in rare cells.

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