Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.
The molecular events that contribute to, and result from, the in vivo binding of transcription factors to their cognate DNA sequence motifs in mammalian genomes are poorly understood. We demonstrate that variations within the DNA sequence motifs that bind the transcriptional repressor REST (NRSF) encode in vivo DNA binding affinity hierarchies that contribute to regulatory function during lineage-specific and developmental programs in fundamental ways. First, canonical sequence motifs for REST facilitate strong REST binding and control functional classes of REST targets that are common to all cell types, whilst atypical motifs participate in weak interactions and control those targets, which are cell- or tissue-specific. Second, variations in REST binding relate directly to variations in expression and chromatin configurations of REST's target genes. Third, REST clearance from its binding sites is also associated with variations in the RE1 motif. Finally, and most surprisingly, weak REST binding sites reside in DNA sequences that show the highest levels of constraint through evolution, thus facilitating their roles in maintaining tissue-specific functions. These relationships have never been reported in mammalian systems for any transcription factor.
Bruce
Alexander W
AW
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom. awb41@cam.ac.uk
López-Contreras
Andrés J
AJ
Flicek
Paul
P
Down
Thomas A
TA
Dhami
Pawandeep
P
Dillon
Shane C
SC
Koch
Christoph M
CM
Langford
Cordelia F
CF
Dunham
Ian
I
Andrews
Robert M
RM
Vetrie
David
D
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D001667:Binding, Competitive; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D006367:HeLa Cells; D006801:Humans; D015151:Immunoblotting; D020014:K562 Cells; D034741:RNA, Small Interfering / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014162:Transfection; D000099229:RE1-Silencing Transcription Factor
D002843:Chromatin; D004247:DNA; D004268:DNA-Binding Proteins; D034741:RNA, Small Interfering; D012097:Repressor Proteins; D000099229:RE1-Silencing Transcription Factor