The PerR of B. subtilis has been well characterized and shown to repress the expression of target genes by binding to conserved promoter sequences known as Per boxes (Chen, Keramati and Helmann 1995).
Within the nucleus, the Smad complex selectively binds to conserved Smad binding element (SBE) DNA sequences, recruits the histone acetyltransferase p300 and other coactivators, and activates or represses the transcription of target genes such as pro-αI (1) collagen (COL1A1) and collagenase-1, respectively [3], [4], [5], [6].
The dRNA-seq identification of TSSs for the majority of the SL1344 genome enabled us to undertake a MEME based analysis of the promoter regions to identify conserved sequences that may represent binding sites for transcriptional regulatory proteins (e.g. sigma factors).
Phosphotyrosine-binding domains are conserved sequences of 100-150 acids acidsubsetubset of which recognize the consensus sequence NPXpY [ 1].
The function(s) of p120 protein family members are targeted to membrane junctional regions where cell-cell interactions occur and include stabilization of cadherins by binding to a highly conserved sequence in the juxtamembrane region [26] [28].
The basic leucine zipper (bZIP) group of TFs like OSBZ8 was earlier reported to target the late embryogenesis abundant (LEA) protein, Rab16A, during salinity stress in indica rice varieties [ 8], through their binding to 8 bp conserved sequence called abscisic acid responsive element (ABRE).
However, the software did not predict a binding site within all conserved sequences.
While the BRD residues important for Kac binding are largely conserved, sequence variations in the ZA and BC loops enable discrimination of different binding targets [5], [6].
MICRA extracts 1 kb of sequence from each binding site, filters it for conserved sequences, and calculates enrichment of the binding site compared to background frequency.
These endeavours provide genome annotation datasets for a range of genome marks, including histone acetylation and methylation [ 5], chromatin states [ 9], DNase hypersensitive sites (DNase HSs) [ 10, 11], DNase footprints [ 12, 13], transcription factor binding sites (TFBSs) [ 14, 15], conserved sequences [ 16], enhancers [ 17] and polymorphisms [ 7].
