ArticleThe Plant cell2022
Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data.
Article in The Plant cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 26 citations in OpenAlex.
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- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Identification of Accessible Transcription Factor Binding Sites During the Seed-to-Seedling Transition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Plant-specific function of H3K9me3 as a permissive chromatin mark during Arabidopsis seed germination.Frontiers in plant science · 2026Article
- Cytokinin-responsive P-type cyclins control Arabidopsis radial style morphology.The Plant journal : for cell and molecular biology · 2025Article
- CRISPR targeting of H3K4me3 activates gene expression and unlocks centromere-proximal crossover recombination in Arabidopsis.Nature communications · 2025Article
- Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches.bioRxiv : the preprint server for biology · 2025Article
- Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach.Plant & cell physiology · 2025Article
- Abscisic acid and GIGANTEA signalling converge to regulate the recruitment of CONSTANS to the FT promoter and activate floral transition.Journal of experimental botany · 2025Article
- VULGARE ROW-TYPE SIX 5 binds to the promoter of tillering and floral homeotic genes to regulate their expression.Plant physiology · 2025Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Wheat NAC transcription factorPlant direct · 2024Article
- Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory in plants.The EMBO journal · 2023Article
- Article
- Epigenetic Control of Plant Response to Heavy Metals.Plants (Basel, Switzerland) · 2023Review
- excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies.Bioinformatics (Oxford, England) · 2023Article
- No more mixed signals: Improved ChIP-seq data analysis with greenscreen.The Plant cell · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to identify factor binding to genomic DNA and chromatin modifications. ChIP-seq data analysis is affected by genomic regions that generate ultra-high artifactual signals. To remove these signals from ChIP-seq data, the Encyclopedia of DNA Elements (ENCODE) project developed comprehensive sets of regions defined by low mappability and ultra-high signals called blacklists for human, mouse (Mus musculus), nematode (Caenorhabditis elegans), and fruit fly (Drosophila melanogaster). However, blacklists are not currently available for many model and nonmodel species. Here, we describe an alternative approach for removing false-positive peaks called greenscreen. Greenscreen is easy to implement, requires few input samples, and uses analysis tools frequently employed for ChIP-seq. Greenscreen removes artifactual signals as effectively as blacklists in Arabidopsis thaliana and human ChIP-seq dataset while covering less of the genome and dramatically improves ChIP-seq peak calling and downstream analyses. Greenscreen filtering reveals true factor binding overlap and occupancy changes in different genetic backgrounds or tissues. Because it is effective with as few as two inputs, greenscreen is readily adaptable for use in any species or genome build. Although developed for ChIP-seq, greenscreen also identifies artifactual signals from other genomic datasets including Cleavage Under Targets and Release Using Nuclease. We present an improved ChIP-seq pipeline incorporating greenscreen that detects more true peaks than other methods.
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