ArticleNucleic acids research2019
DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- PARP1 and PARG Are the Draft Horses for Polycomb-Trithorax Chromatin Regulator Machinery.Biomolecules · 2025Article
- Epigenetic Regulation in Drosophila Tumor Models.Advances in experimental medicine and biology · 2025Review
- Su(Hw) interacts with Combgap to establish long-range chromatin contacts.Epigenetics & chromatin · 2024Article
- Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing.Science advances · 2023Article
- A Green Light to Switch on Genes: Revisiting Trithorax on Plants.Plants (Basel, Switzerland) · 2022Review
- Mode and Tempo of 3D Genome Evolution in Drosophila.Molecular biology and evolution · 2022Article
- Review
- Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3.PloS one · 2022Article
- Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation.Scientific reports · 2021Article
- MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics.BMC bioinformatics · 2021Article
- 3D genome evolution and reorganization in the Drosophila melanogaster species group.PLoS genetics · 2020Article
- ApoPred: Identification of Apolipoproteins and Their Subfamilies With Multifarious Features.Frontiers in cell and developmental biology · 2020Article
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Abstract
Polycomb Response Elements (PREs) are cis-regulatory DNA elements that maintain gene transcription states through DNA replication and mitosis. PREs have little sequence similarity, but are enriched in a number of sequence motifs. Previous methods for modelling Drosophila melanogaster PRE sequences (PREdictor and EpiPredictor) have used a set of 7 motifs and a training set of 12 PREs and 16-23 non-PREs. Advances in experimental methods for mapping chromatin binding factors and modifications has led to the publication of several genome-wide sets of Polycomb targets. In addition to the seven motifs previously used, PREs are enriched in the GTGT motif, recently associated with the sequence-specific DNA binding protein Combgap. We investigated whether models trained on genome-wide Polycomb sites generalize to independent PREs when trained with control sequences generated by naive PRE models and including the GTGT motif. We also developed a new PRE predictor: SVM-MOCCA. Training PRE predictors with genome-wide experimental data improves generalization to independent data, and SVM-MOCCA predicts the majority of PREs in three independent experimental sets. We present 2908 candidate PREs enriched in sequence and chromatin signatures. 2412 of these are also enriched in H3K4me1, a mark of Trithorax activated chromatin, suggesting that PREs/TREs have a common sequence code.
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