ArticleNucleic acids research2023
Sea-ATI unravels novel vocabularies of plant active cistrome.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation.Nucleic acids research · 2025Article
- Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression.aBIOTECH · 2025Article
- Review
- Article
- EGDB: A comprehensive multi-omics database for energy grasses and the epigenomic atlas of pearl millet.iMeta · 2025Article
- Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14.International journal of molecular sciences · 2025Article
- A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet.International journal of molecular sciences · 2024Article
- Decoding complexity: tackling the challenge of how many transcription factors regulate a plant gene.TranscriptionReview
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Authors and funding
16 authors.
Funding
Abstract
The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging. In this study, we report the assay sequential extraction assisted-active TF identification (sea-ATI), a low-input method that profiles the DNA sequences recognized by TFs in a target tissue. We applied sea-ATI to seven plant tissues to survey their active cistrome and generated 41 motif models, including 15 new models that represent previously unidentified cis-regulatory vocabularies. ATAC-seq and RNA-seq analyses confirmed the functionality of the cis-elements from the new models, in that they are actively bound in vivo, located near the transcription start site, and influence chromatin accessibility and transcription. Furthermore, comparing dimeric WRKY CREs between sea-ATI and DAP-seq libraries revealed that thermodynamics and genetic drifts cooperatively shaped their evolution. Notably, sea-ATI can identify not only positive but also negative regulatory cis-elements, thereby providing unique insights into the functional non-coding genome of plants.
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