HDACs are present within multisubunit protein complexes, other components of which govern HDAC target gene specificity by controlling interactions with sequence-specific DNA-binding proteins.
Furthermore, HDACs are part of large protein complexes, which are directed to specific genes via interaction with sequence-specific transcription factors.
Our results are consistent with a model in which mouse or human Dali is recruited to chromatin indirectly via RNA-protein interactions with both sequence-specific transcription factor proteins, such as POU3F3 which is encoded by its neighbouring gene, or non-sequence specific DNA binding cofactors including DNMT1, which in turn may interact with sequence-specific DNA-binding proteins.
With non-random interactions such as those with sequence-specific promoters, a DNA segment can be 'pulled down' with the target protein even when it is not directly bound to it.
By combining histone modifications, including H3K27ac, H3K4me1, and H3K4me3, with sequence-specific features, it achieved an AUC = 0.94.
Another mechanism may be through sequence-specific motifs that direct miRNA trafficking by interaction with specific chaperone proteins (Bolukbasi et al., 2012; Villarroya-Beltri et al., 2013).
Ncl has been shown to activate endogenous Bcl-2 and CD34 gene expression in CD34 positive hematopoietic cells by a direct sequence-specific interaction with the CD34 promoter region and is thus involved in the maintenance of these progenitor/stem cells in hematopoiesis [23].
The miRNAs are endogenous small non-coding RNAs that regulate gene expression by promoting mRNA degradation or preventing translation by imperfect sequence-specific interaction with the 3′-untranslated region of mRNAs.
Additional studies suggest that SSX proteins may also be targeted through direct interactions with chromatin or by binding to sequence-specific transcription factors [ 20, 21].
Lamins bind chromatin through interactions with histones or by directly binding sequence-specific regions of DNA termed matrix-attachment regions (Zhao et al. 1996).
