New paper: Selective loss TF-DNA complex binding as a consequence of compromising DNA shape recognition

February 12, 2020

In this paper, Judith Kribelbauer, who was a joint student with Harmen Bussemaker, significantly extended our understanding of how homeodomain protein complexes (Exd-Hox) bind to the correct binding sites in vivo. Judith generated an amazing amount of data for this paper: high-throughput SELEX-seq assays on wild type and mutant homeodomain proteins, ChIP-seq analyses of tagged homeodomain proteins from wing imaginal discs, and Hi-C data from wing discs to identify enhancer-promoter interactions. As a result, she discovered that compromising the recognition of DNA shape can selectively destabilize a subset of the TF complexes a TF can participate in, allowing her to identify complex-specific binding events and functions.

The other cool thing about these observations is that the same mutations that compromise Exd's ability to recognize DNA shape cause a human disease (CAKUTHED) when they are present in Exd's human ortholog, Pbx1. In other words, we think the CAKUTHED syndrome is caused by a DNA shape recognition mutant.

The abstract of the paper is pasted here:

Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here, we demonstrate that high-throughput in vitro DNA binding assays coupled with unbiased computational analysis provide unprecedented insight into how different DNA sequences select distinct compositions and configurations of homeodomain TF complexes. Using inferred knowledge about minor groove width readout, we design targeted protein mutations that destabilize homeodomain binding both in vitro and in vivo in a complex-specific manner. By performing parallel systematic evolution of ligands by exponential enrichment sequencing (SELEX-seq), chromatin immunoprecipitation sequencing (ChIP-seq), RNA sequencing (RNA-seq), and Hi-C assays, we not only classify the majority of in vivo binding events in terms of complex composition but also infer complex-specific functions by perturbing the gene regulatory network controlled by a single complex.