Binding of S-oligos to heparin binding proteins is sequence-independent but is dependent on the chain length of S-oligos.
Like Pho4, Pho2 and the TATA box binding protein are efficiently excluded from their binding sequences when the latter are wrapped in a nucleosome (Fig. 5, 6).
Affinity precipitation of DNA binding proteins was performed with the optimal binding sequence for AP-1 (5'-CGC TTG ATG AGT CAG CCG GAA-3') (Sigma genosys UK) as previously described [ 37] with the following modifications: total protein content was standardized to 300 – 400 μg/sample using a protein assay (Bio-Rad), according to the manufacturer's instructions.
Bacterial-type transcription factors (TFs) of the helix-turn-helix class of DNA binding proteins are particularly overrepresented in available sequenced archaeal genomes [ 13- 15].
Most of the cation π interactions forming residues in RNA binding proteins are conserved among homologous sequences.
From the list of reconfirmed hits, 45 cDNA clones that were not annotated as encoding general transcription factors (including 9 RNA binding proteins) were selected for further sequence specificity and mechanism of action studies.
Cooperative binding of sequence-specific DNA binding proteins is a cornerstone of transcriptional regulation in eukaryotic genomes (Arnosti and Kulkarni 2005; Wunderlich and Mirny 2009; Martinez and Rao 2012; Ptashne 2013, 2014).
The Runx family of sequence-specific DNA binding proteins are key transcriptional regulators of cell proliferation and differentiation, and are essential for animal development (reviewed by Coffman, 2003; Coffman, 2009).
PAI 1 – The ssrA gene (WS105_tm01) from PAI 1 (Fig. 7) is putatively transcribed into a hybrid transfer messenger RNA (tmRNA) [ 42], whereas the gene encoding the cofactor SmpB (WS105_0199), an SsrA-binding protein, is located elsewhere in the genomic sequence.
PPR proteins are sequence-specific RNA binding proteins that, in plants, bind in a sequence-specific manner to unique organellar mRNAs, resulting in recruitment of enzyme complexes that modulate their expression through post-transcriptional processes, including editing, splicing, translation, and stability [ 67, 69, 70].
