Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6. Issue 23 (24th November 2017)

• Record Type: Journal Article
• Authors: Hu, Caizhen; Malik, Vikas; Chang, Yiming Kenny; Veerapandian, Veeramohan; Srivastava, Yogesh; Huang, Yong-Heng; Hou, Linlin; Cojocaru, Vlad; Stormo, Gary D.; Jauch, Ralf
• Is Part Of: Journal of molecular biology. Volume 429:Issue 23(2017)
• Page Start: 3626
• Page End: 3634
• Publication Date: 2017-11-24
• Subjects: Coop-seq cooperativity-by-sequencing -- TF transcription factor -- HT-SELEX high-throughput systematic evolution of ligands by exponential enrichment -- EMSA electrophoretic mobility shift assay -- ChIP-seq chromatin immunoprecipitation sequencing -- HMG high mobility group -- PRD paired -- PWM position weight matrices -- NPCs neural progenitor cells -- GEO gene expression omnibus -- C/T cell and tissue; cooperativity -- Coop-seq -- gene regulation -- deep sequencing -- Pax6 -- Sox2 -- transcription factors; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2017.10.013
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Sox2 and Pax6 co-regulate genes in neural lineages and the lens by forming a ternary complex likely facilitated allosterically through DNA. We used the quantitative and scalable cooperativity-by-sequencing (Coop-seq) approach to interrogate Sox2/Pax6 dimerization on a DNA library where five positions of the Pax6 half-site were randomized yielding 1024 cooperativity factors. Consensus positions normally required for the high-affinity DNA binding by Pax6 need to be mutated for effective dimerization with Sox2. Out of the five randomized bases, a 5′ thymidine is present in most of the top ranking elements. However, this thymidine maps to a region outside of the Pax half site and is not expected to directly interact with Pax6 in known binding modes suggesting structural reconfigurations. Re-analysis of ChIP-seq data identified several genomic regions where the cooperativity promoting sequence pattern is co-bound by Sox2 and Pax6. A highly conserved Sox2/Pax6 bound site near the Sprouty2 locus was verified to promote cooperative dimerization designating Sprouty2 as a potential target reliant on Sox2/Pax6 cooperativity in several neural cell types. Collectively, the functional interplay of Sox2 and Pax6 demands the relaxation of high-affinity binding sites and is enabled by alternative DNA sequences. We conclude that this binding mode evolved to warrant that a subset of target genes is only regulated in the presence of suitable partner factors. Graphical Abstract: Image 1 Highlights: Quantification of Sox2/Pax6 co-binding to 1024 composite DNA elements The dissolution of the Pax6 consensus motif is critical for Sox2/Pax6 dimerization. A "T" outside the core Pax half-site promotes cooperativity. The Coop-seq signature sequence identifies Sprouty2 as potential Sox2/Pax6 target.