ArticleNucleic acids research2012
Genome-wide polycomb target gene prediction in Drosophila melanogaster.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing.Science advances · 2023Article
- Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3.PloS one · 2022Article
- MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics.BMC bioinformatics · 2021Article
- Genomic organization of Polycomb Response Elements and its functional implication inJournal of biosciences · 2020Article
- DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements.Nucleic acids research · 2019Article
- Three classes of response elements for human PRC2 and MLL1/2-Trithorax complexes.Nucleic acids research · 2018Article
- Mbf1 ensures Polycomb silencing by protectingDevelopment (Cambridge, England) · 2018Article
- Sex combs reduced (Scr) regulatory region of Drosophila revisited.Molecular genetics and genomics : MGG · 2017Article
- The morphogen Decapentaplegic employs a two-tier mechanism to activate target retinal determining genes during ectopic eye formation in Drosophila.Scientific reports · 2016Article
- Combgap contributes to recruitment of Polycomb group proteins in Drosophila.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Effects of EZH2 promoter polymorphisms and methylation status on oral squamous cell carcinoma susceptibility and pathology.American journal of cancer research · 2015Article
- Principles of nucleation of H3K27 methylation during embryonic development.Genome research · 2014Article
- Polycomb group response elements in Drosophila and vertebrates.Advances in genetics · 2013Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
As key epigenetic regulators, polycomb group (PcG) proteins are responsible for the control of cell proliferation and differentiation as well as stem cell pluripotency and self-renewal. Aberrant epigenetic modification by PcG is strongly correlated with the severity and invasiveness of many types of cancers. Unfortunately, the molecular mechanism of PcG-mediated epigenetic regulation remained elusive, partly due to the extremely limited pool of experimentally confirmed PcG target genes. In order to facilitate experimental identification of PcG target genes, here we propose a novel computational method, EpiPredictor, that achieved significantly higher matching ratios with several recent chromatin immunoprecipitation studies than jPREdictor, an existing computational method. We further validated a subset of genes that were uniquely predicted by EpiPredictor by cross-referencing existing literature and by experimental means. Our data suggest that multiple transcription factor networking at the cis-regulatory elements is critical for PcG recruitment, while high GC content and high conservation level are also important features of PcG target genes. EpiPredictor should substantially expedite experimental discovery of PcG target genes by providing an effective initial screening tool. From a computational standpoint, our strategy of modelling transcription factor interaction with a non-linear kernel is original, effective and transferable to many other applications.
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