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Assessing Global Circadian Rhythm Through Single-Time-Point Transcriptomic Analysis

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Modeling Transcriptional Regulation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2328))

Abstract

Plant circadian clock has emerged as a central hub integrating various endogenous signals and exogenous stimuli to coordinate diverse plant physiological processes. The intimate relationship between crop circadian clock and key agronomic traits has been increasingly appreciated. However, due to the lack of fundamental genetic resources, more complex genome structures and the high cost of large-scale time-course circadian expression profiling, our understanding of crop circadian clock is still very limited. To study plant circadian clock, conventional methods rely on time-course experiments, which can be expensive and time-consuming. Different from these conventional approaches, the molecular timetable method can estimate the global rhythm using single-time-point transcriptome datasets, which has shown great promises in accelerating studies of crop circadian clock. Here we describe the application of the molecular timetable method in soybean and provide key technical caveats as well as related R Markdown scripts.

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Acknowledgment

This work was supported by the funds from State Key Laboratory for Protein and Plant Gene Research, Peking University, Center for Life Sciences and the National Natural Science Foundation of China (31970641) to W.W. and the funds from Beijing Nova Program of Science and Technology (Z191100001119027) and the National Natural Science Foundation of China (31970283) to M. Z.

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Authors and Affiliations

  1. State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China

    Xingwei Wang & Wei Wang

  2. Center for Life Sciences, Beijing, China

    Xingwei Wang & Wei Wang

  3. College of Life Sciences, Capital Normal University, Beijing, China

    Yufeng Xu & Mian Zhou

Authors
  1. Xingwei Wang
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  2. Yufeng Xu
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  3. Mian Zhou
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  4. Wei Wang
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Corresponding authors

Correspondence to Mian Zhou or Wei Wang .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Alabama, Birmingham, AL, USA

    SHAHID MUKHTAR

1 Electronic Supplementary Materials

Data 1

List of soybean time-indicating genes. A reference sequence for RASL-seq used in this study. 40 nucleotides of 288 target genes are sequentially joined for the downstream bioinformatics analysis, including the read alignment and count (CSV 92 kb)

Data 2

Demo expression matrix of soybean transcriptome dataset (CSV 4558 kb)

Data 3

R Markdown demonstration of the molecular timetable and related statistical analysis (PDF 734 kb)

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Wang, X., Xu, Y., Zhou, M., Wang, W. (2021). Assessing Global Circadian Rhythm Through Single-Time-Point Transcriptomic Analysis. In: MUKHTAR, S. (eds) Modeling Transcriptional Regulation. Methods in Molecular Biology, vol 2328. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1534-8_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1534-8_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1533-1

  • Online ISBN: 978-1-0716-1534-8

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