Extensive conservation of sequences and chromatin structures in the bxd polycomb response element among Drosophilid species

The Polycomb Response Element (PRE) is the nucleation site for the Polycomb silencing complexes. The sequences responsible for the recruitment of the components of the Polycomb complex are not well understood. A comparison of the bxd PRE sequences from several different Drosophila species shows that some changes have occurred during phylogeny but large blocks of sequence are conserved after a divergence of some 60 million years. We compare the PRE sequences, the sites of some known PRE binding proteins, the conservation of DNasel hypersensitive sites and relate them to the sequence of the Ultrabithorax promoter which these PREs regulate.     

Transactivation specificity is conserved among p53 family proteins and depends on a response element sequence code

Structural and biochemical studies have demonstrated that p73, p63 and p53 recognize DNA with identical amino acids and similar binding affinity. Here, measuring transactivation activity for a large number of response elements (REs) in yeast and human cell lines, we show that p53 family proteins also have overlapping transactivation profiles. We identified mutations at conserved amino acids of loops L1 and L3 in the DNA-binding domain that tune the transactivation potential nearly equally in p73, p63 and p53. For example, the mutant S139F in p73 has higher transactivation potential towards selected REs, enhanced DNA-binding cooperativity in vitro and a flexible loop L1 as seen in the crystal structure of the protein–DNA complex. By studying, how variations in the RE sequence affect transactivation specificity, we discovered a RE-transactivation code that predicts enhanced transactivation; this correlation is stronger for promoters of genes associated with apoptosis.     

Staining efficiency of specific proteins depends on the staining method: wheat gluten proteins

To analyze gluten proteins involved in celiac disease (CD) by proteomic analysis, prolamins extracted from hexaploid wheat varieties were analyzed by SDS-PAGE and 2-DE. Differences between staining methods (CBB, silver nitrate, SYPRO Ruby, and CyDye) were analyzed in comparison to immunoblotting. Staining efficiency varied per protein across methods, and complete staining of all gluten proteins could not be achieved by one of these methods. Care should be taken in the selection of staining method especially if one wants to relate the results to data obtained by immunoblotting.