ArticlePlant physiology2014
A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification.
Article in Plant physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
- The canonical E2Fs together with RETINOBLASTOMA-RELATED are required to establish quiescence during plant development.Communications biology · 2023Article
- Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.Nature plants · 2021Article
- The F-Box-Like Protein FBL17 Is a Regulator of DNA-Damage Response and Colocalizes with RETINOBLASTOMA RELATED1 at DNA Lesion Sites.Plant physiology · 2020Article
- Building a Robust Chromatin Immunoprecipitation Method with Substantially Improved Efficiency.Plant physiology · 2020Article
- Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth.Plant biotechnology journal · 2020Article
- RETRACTED: Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators.PLoS genetics · 2018Article
- GSPlant physiology · 2018Article
- The reduction in maize leaf growth under mild drought affects the transition between cell division and cell expansion and cannot be restored by elevated gibberellic acid levels.Plant biotechnology journal · 2018Article
- JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.Nucleic acids research · 2018Article
- Making a Better Home: Modulation of Plant Defensive Response byFrontiers in plant science · 2018Article
- The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis.Nature communications · 2017Article
- Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3 levels in dividing cells inProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Enhancing gene regulatory network inference through data integration with markov random fields.Scientific reports · 2017Article
- Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development.Journal of experimental botany · 2016Article
- SUPPRESSOR OF PHYTOCHROME B4-#3 Represses Genes Associated with Auxin Signaling to Modulate Hypocotyl Growth.Plant physiology · 2016Article
- A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.Plant physiology · 2016Article
- A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis.The Plant cell · 2015Article
- An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes.Nature protocols · 2015Article
- The ASH1-RELATED3 SET-domain protein controls cell division competence of the meristem and the quiescent center of the Arabidopsis primary root.Plant physiology · 2014Article
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Authors and funding
13 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation, this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis (Arabidopsis thaliana) cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional chromatin immunoprecipitation and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and coexpression network analyses demonstrates the quality of the E2Fa TChAP sequencing data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.