Judith F. Kribelbauer-Swietek, Olga Pushkarev, Vincent Gardeux, Katerina Faltejskova, Julie Russeil et al.
Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription factor (TF) binding instruct the formation of high regulatory factor environments remains poorly understood. Here we developed a new approach leveraging enhancer-centric chromatin accessibility quantitative trait loci (caQTLs) to nominate regulatory factor clusters genome-wide. By analyzing TF-binding signatures within the context of caQTLs and comparing episomal versus endogenous enhancer activities, we discovered a class of regulators, ‘context-only’ TFs, that amplify the activity of cell type-specific caQTL-binding TFs, that is, ‘context-initiator’ TFs. Similar to super-enhancers, enhancers enriched for context-only TF-binding sites display high coactivator binding and sensitivity to bromodomain-inhibiting molecules. We further show that binding sites for context-only and context-initiator TFs underlie enhancer coordination, providing a mechanistic rationale for how a loose TF syntax confers regulatory specificity.
Judith F. Kribelbauer-Swietek, Olga Pushkarev, Vincent Gardeux, Katerina Faltejskova, Julie Russeil, Guido van Mierlo, Bart Deplancke. Context transcription factors establish cooperative environments and mediate enhancer communication. 2024-10-03. https://doi.org/10.1038/s41588-024-01892-7
A synthetic library of 110-bp random-context inserts containing homotypic and heterotypic repeats of eight TF motifs with 10-bp spacers and 12-bp random barcodes was transfected episomally into MEC-1. The table summarizes each sequence construct’s barcode-normalized RNA/DNA activity in two RNA replicates.
A 270-bp allele-aware library of caQTL lead and linked neighbor/dependent enhancer fragments was assayed for autonomous promoter activity in GM12878 using the SuRE barcoded plasmid assay. The table reports QC-filtered element/genotype groups with sequence, variant annotation, count-derived activity, and zero-RNA fractions.
A synthetic library of 110-bp random-context inserts containing homotypic and heterotypic repeats of eight TF motifs with 5-bp spacers and 12-bp random barcodes was transfected episomally into MEC-1. The table summarizes each sequence construct’s barcode-normalized RNA/DNA activity in two RNA replicates.
The 5-bp synthetic STARR-seq library was integrated by Cre-recombinase cassette exchange into an AXIN2 landing pad in MEC-1 cells. The table summarizes QC-filtered construct-level gDNA-normalized mRNA activity, expression fraction, coverage, and no-TFBS-relative activity.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 12 files (ZIP)README.txtSTARRseq_10bp_library_sequences_and_TF_syntax.csvSTARRseq_5bp_fragment_summary_author.csvSTARRseq_5bp_library_sequences_and_TF_syntax.csvSTARRseq_endogenous_BC_counts.csvSTARRseq_episomal_raw_counts_10bp.csv.gzSTARRseq_episomal_raw_counts_5bp.csv.gzsupplementary_information.pdfSuRE_raw_Fwd.txt.gzSuRE_raw_Rev.txt.gzSuRE_sequences.csvzenodo_README.txt