REVEALING THE HUMAN PROMOTEROME

A comparative genomics analysis of the human promoterome has been performed using our transcription factor binding site (TFBS) footprinting method.  Through matrix-scoring of aligned mammal promoters, we have identified potential TFBSs that are conserved across these species.

Transcription start sites (TSSs) of 76,165 human protein-coding transcripts were used to identify alignments of mammal promoter sequences.  These alignments were then retrieved from the Ensembl database (http://www.ensembl.org).  The Jaspar database (http://jaspar.genereg.net/) was used to create position weight matrices (PWMs) for a total of 519 transcription factors.  All species’ sequences in each alignment retrieved for each promoter region were then scored using the PWMs.  Predictions with a score above a threshold corresponding to a p-value of 0.001 which were observed in human and at least one other species, were kept for comparison with other conserved binding sites.