Short tandem repeats bind transcription factors to tune eukaryotic gene expression

• 成果类型: Article
• 署名作者: Horton, Connor A.; Alexandari, Amr M.; Hayes, Michael G. B.; Marklund, Emil; Schaepe, Julia M.; Aditham, Arjun K.; Shah, Nilay; Suzuki, Peter H.; Shrikumar, Avanti; Afek, Ariel; Greenleaf, William J.; Gordan, Raluca; Zeitlinger, Julia; Kundaje, Anshul; Fordyce, Polly M.
• 署名单位: Stanford University; Stanford University; Stanford University; Stanford University; Stowers Institute for Medical Research; Duke University; Duke University; Weizmann Institute of Science; Duke University; Duke University; University of Kansas; University of Kansas Medical Center; Chan Zuckerberg Initiative (CZI); University of California System; University of California Berkeley; Fred Hutchinson Cancer Center
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-13289
• DOI: 10.1126/science.add1250
• 发表日期: 2023-09-22
• 页码: 1304-+
• 关键词: intrinsically disordered regions; protein-dna binding; polymorphic microsatellite; spontaneous mutations; dinucleotide repeat; regulatory proteins; promoter activity; high-resolution; sequence; specificity

摘要

Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.