Single-Cell RNA Sequencing Efficiently Predicts Transcription Factor Targets in Plants

Overview

Journal Front Plant Sci

Date 2021 Jan 11

PMID 33424903

Citations 9

Authors

Yunjie Xie

Shenfei Jiang

Lele Li

Xiangzhen Yu

YuPeng Wang

Cuiqin Luo

Qiuhua Cai

Wei He

Hongguang Xie

Yanmei Zheng

Huaan Xie

Jianfu Zhang

Affiliations

Soon will be listed here.

Abstract

Discovering transcription factor (TF) targets is necessary for the study of regulatory pathways, but it is hampered in plants by the lack of highly efficient predictive technology. This study is the first to establish a simple system for predicting TF targets in rice () leaf cells based on 10 × Genomics' single-cell RNA sequencing method. We effectively utilized the transient expression system to create the differential expression of a TF (OsNAC78) in each cell and sequenced all single cell transcriptomes. In total, 35 candidate targets having strong correlations with OsNAC78 expression were captured using expression profiles. Likewise, 78 potential differentially expressed genes were identified between clusters having the lowest and highest expression levels of OsNAC78. A gene overlapping analysis identified 19 genes as final candidate targets, and various assays indicated that Os01g0934800 and Os01g0949900 were OsNAC78 targets. Additionally, the cell profiles showed extremely similar expression trajectories between OsNAC78 and the two targets. The data presented here provide a high-resolution insight into predicting TF targets and offer a new application for single-cell RNA sequencing in plants.

Citing Articles

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References

Jean-Baptiste K, McFaline-Figueroa J, Alexandre C, Dorrity M, Saunders L, Bubb K . Dynamics of Gene Expression in Single Root Cells of . Plant Cell. 2019; 31(5):993-1011. PMC: 8516002. DOI: 10.1105/tpc.18.00785. View

Denyer T, Ma X, Klesen S, Scacchi E, Nieselt K, Timmermans M . Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing. Dev Cell. 2019; 48(6):840-852.e5. DOI: 10.1016/j.devcel.2019.02.022. View

Macosko E, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M . Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214. PMC: 4481139. DOI: 10.1016/j.cell.2015.05.002. View

Zhang T, Xu Z, Shang G, Wang J . A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root. Mol Plant. 2019; 12(5):648-660. DOI: 10.1016/j.molp.2019.04.004. View

Barski A, Zhao K . Genomic location analysis by ChIP-Seq. J Cell Biochem. 2009; 107(1):11-8. PMC: 3839059. DOI: 10.1002/jcb.22077. View

Kolodziejczyk A, Kim J, Svensson V, Marioni J, Teichmann S . The technology and biology of single-cell RNA sequencing. Mol Cell. 2015; 58(4):610-20. DOI: 10.1016/j.molcel.2015.04.005. View

Yang G, Chao D, Ming Z, Xia J . A Simple Method to Detect the Inhibition of Transcription Factor-DNA Binding Due to Protein-Protein Interactions In Vivo. Genes (Basel). 2019; 10(9). PMC: 6770856. DOI: 10.3390/genes10090684. View

Ryu K, Huang L, Kang H, Schiefelbein J . Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells. Plant Physiol. 2019; 179(4):1444-1456. PMC: 6446759. DOI: 10.1104/pp.18.01482. View

Nuruzzaman M, Sharoni A, Kikuchi S . Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Front Microbiol. 2013; 4:248. PMC: 3759801. DOI: 10.3389/fmicb.2013.00248. View

10.

Wagner U, Edwards R, Dixon D, Mauch F . Probing the diversity of the Arabidopsis glutathione S-transferase gene family. Plant Mol Biol. 2002; 49(5):515-32. DOI: 10.1023/a:1015557300450. View

11.

Perna A, Auber Alberi L . TF-ChIP Method for Tissue-Specific Gene Targets. Front Cell Neurosci. 2019; 13:95. PMC: 6433963. DOI: 10.3389/fncel.2019.00095. View

12.

Zhang Y, Su J, Duan S, Ao Y, Dai J, Liu J . A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes. Plant Methods. 2011; 7(1):30. PMC: 3203094. DOI: 10.1186/1746-4811-7-30. View

13.

Papalexi E, Satija R . Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol. 2017; 18(1):35-45. DOI: 10.1038/nri.2017.76. View

14.

Ernst H, Olsen A, Larsen S, Lo Leggio L . Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors. EMBO Rep. 2004; 5(3):297-303. PMC: 1299004. DOI: 10.1038/sj.embor.7400093. View

15.

Sun L, Huang L, Hong Y, Zhang H, Song F, Li D . Comprehensive analysis suggests overlapping expression of rice ONAC transcription factors in abiotic and biotic stress responses. Int J Mol Sci. 2015; 16(2):4306-26. PMC: 4346958. DOI: 10.3390/ijms16024306. View

16.

Olsen T, Baryawno N . Introduction to Single-Cell RNA Sequencing. Curr Protoc Mol Biol. 2018; 122(1):e57. DOI: 10.1002/cpmb.57. View

17.

Dean J, Goodwin P, Hsiang T . Induction of glutathione S-transferase genes of Nicotiana benthamiana following infection by Colletotrichum destructivum and C. orbiculare and involvement of one in resistance. J Exp Bot. 2005; 56(416):1525-33. DOI: 10.1093/jxb/eri145. View

18.

Luo Q, Han W, Zhou Y, Yao Y, Li Z . The 3D structure of the defense-related rice protein Pir7b predicted by homology modeling and ligand binding studies. J Mol Model. 2008; 14(7):559-69. DOI: 10.1007/s00894-008-0310-3. View

19.

Welner D, Lindemose S, Grossmann J, Mollegaard N, Olsen A, Helgstrand C . DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors. Biochem J. 2012; 444(3):395-404. DOI: 10.1042/BJ20111742. View

20.

NELSON H . Structure and function of DNA-binding proteins. Curr Opin Genet Dev. 1995; 5(2):180-9. DOI: 10.1016/0959-437x(95)80006-9. View