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Mol Cell. 2020 Feb 6. pii: S1097-2765(20)30048-4. doi: 10.1016/j.molcel.2020.01.027. [Epub ahead of print]

Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins.

Author information

1
Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.
2
Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
3
Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address: hjb2004@columbia.edu.
4
Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA. Electronic address: rsm10@columbia.edu.

Abstract

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.

KEYWORDS:

3D nuclear architecture; ChIP-seq; DNA binding specificity; DNA shape; Hox cofactors; Hox proteins; antennapedia; homeodomain protein binding; in vivo transcription factor binding; minor groove recognition; transcription factor complexes; wing imaginal disc development

Conflict of interest statement

Declaration of Interests The authors declare no competing interests.

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