This workflow was applied to profile the specificity of PTM-specific antibodies, histone binding proteins, and histone modifying enzymes.
Specifically, RA binding to RARα triggers both the dissociation of corepressors proteins, and the recruitment of coactivators and histone modifying enzymes that enable chromatin conformation changes compatible with the access and action of RNA polymerase II [4], [5].
The ENCODE project generated genome-wide DNA binding data for 119 proteins, including sequence-specific TFs, general TFs, RNA polymerases II (Pol II) and III, and histone modifying complexes, in dozens of human cell lines/types [20].
A wide range of modifying activities acts on nucleosome, a central unit of chromatin, including histone chaperones, ATP-dependent chromatin remodeling factors (remodelers), and histone modifying enzymes.
These marks guide the recruitment and binding of defined histone modifying enzymes and other regulatory proteins [ 16].
DNA methylation mediates gene silencing primarily by inducing repressive chromatin architecture via a common theme of interaction involving methyl-CpG binding (MBD) proteins, histone modifying enzymes and chromatin remodelling complexes.
These observations support the hypothesis that the effect of DNA methylation, i.e. either causing a repressed (heterochromatin) or open (euchromatin) chromatin state, can vary depending on the species, sequence context, DNA binding proteins, and the histone modifying enzymes that are associated with methylated DNA [ 16, 24].
Zika, E. & Ting, J. P. Epigenetic control of MHC-II: interplay between CIITA and histone-modifying enzymes.
Nekrasov, M., Wild, B. & Müller, J. Nucleosome binding and histone methyltransferase activity of Drosophila PRC2.
The human herpes simplex virus-associated host cell factor 1 (HCF-1) is a conserved human transcriptional co-regulator that links positive and negative histone modifying activities with sequence-specific DNA-binding transcription factors.
