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Series GSE125604 Query DataSets for GSE125604
Status Public on Jan 27, 2020
Title Context-dependent gene regulation by homeodomain transcription factor complexes revealed by shape-readout deficient proteins
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Expression profiling by high throughput sequencing
Summary 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.
 
Overall design SELEX-seq was performed on different combinations of the three homeodomain transcription factors Deformed, Homothorax and Extradenticle for both wild-type and shape-readout-impaired mutant protein. In addition, ATAC-seq and ChIP-seq was performed in D.melanogaster 3rd instar imaginal wing discs against both wild-type and shape-readout mutant Extradenticle, as well as Homothorax and Antennapedia TFs. Intrinsic DNA Shape (Zhou, PNAS, 2015) was correlated with TF binding affinity to identify position-specific shape readout (minor groove readout). Amino acid mutations abolishing the identified shape readout were subsequently used in vitro and in vivo to probe the degree to which binding mechanism are recapitulated in vivo. Further Hi-C and RNA-seq data was used to dissect the regulatory network of HD TF complexes and identify complex-specific gene function.
 
Contributor(s) Mann RS, Bussemaker HJ, Kribelbauer JF
Citation(s) 32053778
Submission date Jan 24, 2019
Last update date Jun 03, 2020
Contact name Harmen J Bussemaker
Organization name Columbia University
Department Biological Sciences
Lab Bussemaker Lab
Street address 1212 Amsterdam Avenue, MC 2441
City New York City
State/province New York
ZIP/Postal code 10027
Country USA
 
Platforms (2)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (33)
GSM3578064 R0_Hth_Exd_Dfd_wt_mut_Lib21_HthF_HthR_SELEX_seq
GSM3578065 R0_Hth_Exd_Dfd_wt_Lib30_SELEX_seq
GSM3578066 R0_Hth_Exd_wt_mut_Lib16_SELEX_seq
Relations
BioProject PRJNA516909
SRA SRP181908

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125604_RAW.tar 2.2 Gb (http)(custom) TAR (of BED, BW, HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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