Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6

Caizhen Hu, Vikas Malik, Yiming Kenny Chang, Veeramohan Veerapandian, Yogesh Srivastava, Yong Heng Huang, Linlin Hou, Vlad Cojocaru, Gary D. Stormo, Ralf Jauch

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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.

Original languageEnglish
Pages (from-to)3626-3634
Number of pages9
JournalJournal of Molecular Biology
Issue number23
StatePublished - Nov 24 2017


  • Coop-seq
  • Pax6
  • Sox2
  • cooperativity
  • deep sequencing
  • gene regulation
  • transcription factors


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