Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq

© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes.Link_to_subscribed_fulltex

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

© 2017 Elsevier Ltd 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.Link_to_subscribed_fulltex

Microgel-Enhanced Double Network Hydrogel Electrode with High Conductivity and Stability for Intrinsically Stretchable and Flexible All-Gel-State Supercapacitor

In the present work, a new strategy is proposed to simultaneously enhance the toughness and electrochemical performance of the hydrogel with conductive microgel to form microgel-reinforced double network hydrogel. In this hydrogel, the conductive microgel is cross-linked to form the first network, which can dissipate energy to improve mechanical performance and stabilize the conductive network to improve the electrochemical performance. These hydrogels show excellent mechanical properties and good conductivity. When these hydrogels are assembled to all-gel-state intrinsically flexible and stretchable supercapacitor, they deliver outstanding capacitance. The strategy put forward here can extend the application scope of the hydrogel with multifunction

Microgel-Enhanced Double Network Hydrogel Electrode with High Conductivity and Stability for Intrinsically Stretchable and Flexible All-Gel-State Supercapacitor

In the present work, a new strategy is proposed to simultaneously enhance the toughness and electrochemical performance of the hydrogel with conductive microgel to form microgel-reinforced double network hydrogel. In this hydrogel, the conductive microgel is cross-linked to form the first network, which can dissipate energy to improve mechanical performance and stabilize the conductive network to improve the electrochemical performance. These hydrogels show excellent mechanical properties and good conductivity. When these hydrogels are assembled to all-gel-state intrinsically flexible and stretchable supercapacitor, they deliver outstanding capacitance. The strategy put forward here can extend the application scope of the hydrogel with multifunction

Microgel-Enhanced Double Network Hydrogel Electrode with High Conductivity and Stability for Intrinsically Stretchable and Flexible All-Gel-State Supercapacitor

In the present work, a new strategy is proposed to simultaneously enhance the toughness and electrochemical performance of the hydrogel with conductive microgel to form microgel-reinforced double network hydrogel. In this hydrogel, the conductive microgel is cross-linked to form the first network, which can dissipate energy to improve mechanical performance and stabilize the conductive network to improve the electrochemical performance. These hydrogels show excellent mechanical properties and good conductivity. When these hydrogels are assembled to all-gel-state intrinsically flexible and stretchable supercapacitor, they deliver outstanding capacitance. The strategy put forward here can extend the application scope of the hydrogel with multifunction