DNA specificity determinants associate with distinct transcription factor functions.
To elucidate how genomic sequences build transcriptional control networks, we need to understand the connection between DNA sequence and transcription factor binding and function. Binding predictions based solely on consensus predictions are limited, because a single factor can use degenerate sequence motifs and because related transcription factors often prefer identical sequences. The ETS family transcription factor, ETS1, exemplifies these challenges. Unexpected, redundant occupancy of ETS1 and other ETS proteins is observed at promoters of housekeeping genes in T cells due to common sequence preferences and the presence of strong consensus motifs. However, ETS1 exhibits a specific function in T cell activation; thus, unique transcriptional targets are predicted. To uncover the sequence motifs that mediate specific functions of ETS1, a genome-wide approach, chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), identified both promoter and enhancer binding events in Jurkat T cells. A comparison with DNase I sensitivity both validated the dataset and also improved accuracy. Redundant occupancy of ETS1 with the ETS protein GABPA occurred primarily in promoters of housekeeping genes, whereas ETS1 specific occupancy occurred in the enhancers of T cell-specific genes. Two routes to ETS1 specificity were identified: an intrinsic preference of ETS1 for a variant of the ETS family consensus sequence and the presence of a composite sequence that can support cooperative binding with a RUNX transcription factor. Genome-wide occupancy of RUNX factors corroborated the importance of this partnership. Furthermore, genome-wide occupancy of co-activator CBP indicated tight co-localization with ETS1 at specific enhancers, but not redundant promoters. The distinct sequences associated with redundant versus specific ETS1 occupancy were predictive of promoter or enhancer location and the ontology of nearby genes. These findings demonstrate that diversity of DNA binding motifs may enable variable transcription factor function at different genomic sites.
Hollenhorst
Peter C
PC
Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America.
Chandler
Katherine J
KJ
Poulsen
Rachel L
RL
Johnson
W Evan
WE
Speck
Nancy A
NA
Graves
Barbara J
BJ
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D050657:Core Binding Factor alpha Subunits / Q000378:metabolism / Q000502:physiology*; D004742:Enhancer Elements, Genetic; D051268:GA-Binding Protein Transcription Factor; D053263:Gene Regulatory Networks; D015894:Genome, Human; D006801:Humans; D019169:Jurkat Cells; D008213:Lymphocyte Activation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D050784:Proto-Oncogene Protein c-ets-1 / Q000378:metabolism / Q000502:physiology*; D013601:T-Lymphocytes; D014157:Transcription Factors / Q000378:metabolism / Q000502:physiology*
D050657:Core Binding Factor alpha Subunits; D051268:GA-Binding Protein Transcription Factor; C495661:GABPA protein, human; D050784:Proto-Oncogene Protein c-ets-1; D014157:Transcription Factors