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EpiFactors is a database for epigenetic factors, corresponding genes and products. Epigenetic factors are defined as:
  • Proteins that change the general structure of chromatin (chromatin remodeling), including
    • Proteins that act upon post-translational modifications of histones (histone modification read, write and erase);
    • Proteins that move, eject or restructure nucleosomes (ATP-dependent chromatin remodelers);
    • Proteins that incorporate histone variants into the nucleosomes.
    Specific subgroups of proteins may be annotated as such, e.g. the Polycomb group (PcG) proteins.
  • Protein cofactors forming complexes with epigenetic factors, where complex formation is important for the activity (cofactor).
  • Proteins acting as histones, histone variants or protamines (histone).
  • Proteins assisting histone folding and assembly (histone chaperone).
  • Proteins that act upon modifications of DNA or RNA in such a way that it affects gene expression, but not throught RNA processing (DNA or RNA modification).
  • LncRNAs that are involved in epigenetic regulation by various mechanisms, including
    • Recruitment or sequestration of a chromatin modifiers;
    • Chromatin loop formation by recruitment of looping factors or R-loop formation;
    • Regulation of alternative splicing by modification, recruitment or sequestration of splicing factors, chromatin remodeling or R-loop formation;
    • miRNA sequestration (sponging).
EpiFactors: a comprehensive database of human epigenetic factors and complexes.
Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, The FANTOM Consortium and Finn Drabløs.
Database (2015) 2015 : bav067; doi: 10.1093/database/bav067
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes.
Daria Marakulina, Ilya E Vorontsov, Ivan V Kulakovskiy, Andreas Lennartsson, Finn Drabløs and Yulia A Medvedeva.
Nucleic Acids Research (2022); doi: 10.1093/nar/gkac989