Transient ChIP-Seq for Genome-wide In Vivo DNA Binding Landscape

Wang, Guan-Qun; Li, Xiaozheng; An, Yunyun; Zhang, Jianhua; Li, Haoxuan

doi:10.1016/j.tplants.2020.12.002

Cited by 6 publications

(4 citation statements)

References 8 publications

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“…Transient ChIP‐qPCR is a fast and important method for studying protein–DNA binding in vivo and has been widely used in different species of plants (Lee et al ., 2017; Wang et al ., 2021). Fully extended leaves of N .…”

Section: Methodsmentioning

confidence: 99%

“…Transient ChIP-qPCR is a fast and important method for studying protein-DNA binding in vivo and has been widely used in different species of plants (Lee et al, 2017;Wang et al, 2021). Fully extended leaves of N. benthamiana were infiltrated with Agrobacterium strain GV3101 with NbABI5-cMyc (OD 600 % 0.6), and treated with ABA (100 µM) at 48 hpi.…”

Section: Yeast One-hybrid Assay and Transient Chip-qpcrmentioning

confidence: 99%

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Ferredoxin 1 is downregulated by the accumulation of abscisic acid in an ABI5‐dependent manner to facilitate rice stripe virus infection in Nicotiana benthamiana and rice

Cui

Wang²,

Han

et al. 2021

The Plant Journal

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Summary Ferredoxin 1 (FD1) accepts and distributes electrons in the electron transfer chain of plants. Its expression is universally downregulated by viruses and its roles in plant immunity have been brought into focus over the past decade. However, the mechanism by which viruses regulate FD1 remains to be defined. In a previous report, we found that the expression of Nicotiana benthamiana FD1 (NbFD1) was downregulated following infection with potato virus X (PVX) and that NbFD1 regulates callose deposition at plasmodesmata to play a role in defense against PVX infection. We now report that NbFD1 is downregulated by rice stripe virus (RSV) infection and that silencing of NbFD1 also facilitates RSV infection, while viral infection was inhibited in a transgenic line overexpressing NbFD1, indicating that NbFD1 also functions in defense against RSV infection. Next, a RSV‐derived small interfering RNA was identified that contributes to the downregulation of FD1 transcripts. Further analysis showed that the abscisic acid (ABA) which accumulates in RSV‐infected plants also represses NbFD1 transcription. It does this by stimulating expression of ABA insensitive 5 (ABI5), which binds the ABA response element motifs in the NbFD1 promoter, resulting in negative regulation. Regulation of FD1 by ABA was also confirmed in RSV‐infected plants of the natural host rice. The results therefore suggest a mechanism by which virus regulates chloroplast‐related genes to suppress their defense roles.

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Section: Methodsmentioning

confidence: 99%

Section: Yeast One-hybrid Assay and Transient Chip-qpcrmentioning

confidence: 99%

Ferredoxin 1 is downregulated by the accumulation of abscisic acid in an ABI5‐dependent manner to facilitate rice stripe virus infection in Nicotiana benthamiana and rice

Cui

Wang²,

Han

et al. 2021

The Plant Journal

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show abstract

“…However, conventional methods for genome‐wide profiling of transcription factor binding sites (TFBSs), such as chromatin immunoprecipitation sequencing (ChIP‐seq), are limited by the need for stable transgenic materials. Conventional methods can also be time consuming, costly, and low‐throughput (Wang et al, 2021). Although high‐throughput DNA affinity purification sequencing (DAP‐seq) has been developed to directly determine genome‐wide TFBSs in vitro , it is costly and cannot be performed in vivo (Bartlett et al, 2017; Galli et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…However, conventional methods for genome-wide profiling of transcription factor binding sites (TFBSs), such as chromatin immunoprecipitation sequencing (ChIP-seq), are limited by the need for stable transgenic materials. Conventional methods can also be time consuming, costly, and low-throughput (Wang et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

A cost‐effective tsCUT&Tag method for profiling transcription factor binding landscape

Luo

Shi

et al. 2022

JIPB

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Knowledge of the transcription factor binding landscape (TFBL) is necessary to analyze gene regulatory networks for important agronomic traits. However, a low‐cost and high‐throughput in vivo chromatin profiling method is still lacking in plants. Here, we developed a transient and simplified cleavage under targets and tagmentation (tsCUT&Tag) that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction. Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP‐seq. Furthermore, we developed a strategy combining tsCUT&Tag with machine learning, which has great potential for profiling the TFBL across plant development.

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AaHY5 ChIP-seq based on transient expression system reveals the role of AaWRKY14 in artemisinin biosynthetic gene regulation

Zhou

Huang

Wang

et al. 2021

Plant Physiology and Biochemistry

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Transient ChIP-Seq for Genome-wide In Vivo DNA Binding Landscape

Cited by 6 publications

References 8 publications

Ferredoxin 1 is downregulated by the accumulation of abscisic acid in an ABI5‐dependent manner to facilitate rice stripe virus infection in Nicotiana benthamiana and rice

Ferredoxin 1 is downregulated by the accumulation of abscisic acid in an ABI5‐dependent manner to facilitate rice stripe virus infection in Nicotiana benthamiana and rice

A cost‐effective tsCUT&Tag method for profiling transcription factor binding landscape

AaHY5 ChIP-seq based on transient expression system reveals the role of AaWRKY14 in artemisinin biosynthetic gene regulation

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