Recent in silico prediction of cis-sequences over-represented in Fe deficiency-induced gene promoters revealed that the IDEF1-, IDEF2-, and OsIRO2-binding sequences are enriched within the 500-bp promoter regions of Fe deficiency-induced genes (Kakei et al. [2013]; Ogo et al. [2014]).
Although both tele- and proximal heart enhancers are enriched for the binding motifs of several cardiac transcription factors (TFs) (such as MEF2A), tele-enhancer sequences are enriched for TEAD1 and NKX-2.5 binding motifs and are depleted of the GATA4 binding motif compared with proximal enhancers.
The cDNA sequences are enriched in the following gene ontology functional categories: protein binding, hydrolase, transferase, and catalytic enzymes.
In order confirm that E-box binding consensus sequences were enriched throughout the ChIP-seq datasets for E12.5 ECCs, E10.5 limb buds, and PNST cells de-novo motif analysis was performed using PscanChIP, which utilizes the TRANSFAC database, and MEME-ChIP, which utilizes the JASPAR database [ 18, 19].
This indicated that NFI binding sequences are not significantly enriched at mouse promoters as compared to intergenic and transcribed regions, but that it is the association to the binding sites per se that occurs preferentially at promoters.
These data demonstrate that A-type lamin-interacting gene promoters preferentially localize in genomic clusters, lack unique consensus lamin A-binding sequences, and are enriched for a small set of specific transcription factor binding motifs.
We confirmed that the canonical E2F4 binding sequence was highly enriched in the E2F4 bound promoter regions.
A recent report demonstrated that ETS1-binding sequences were specifically enriched in AR-targeted genes [107].
Thus, combinatorial Insm1/Neurod1/Foxa2 binding sites are enriched for sequences implicated in β-cell dysfunction in humans.
A TF is resampled only if it is expressed in K562 cells, and if its binding sequence motif is enriched (p-value <10−7) in the target gene (within 1kb of the transcription start site).
