Chang Yiming K, Srivastava Yogesh, Hu Caizhen, Joyce Adam, Yang Xiaoxiao, Zuo Zheng, Havranek James J, Stormo Gary D, Jauch Ralf
Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
Nucleic Acids Res. 2017 Jan 25;45(2):832-845. doi: 10.1093/nar/gkw1198. Epub 2016 Dec 2.
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.
已知转录因子的协同结合在赋予细胞特性的基因表达程序调控中很重要。然而，目前测量协同参数的方法费力，因此一次仅限于研究少数序列变体。我们开发了Coop-seq（通过测序测定协同性），它能够在单个实验中高效、准确地确定数百种不同DNA序列的协同参数。我们使用324个具有改变的半位点方向、改变的间距和结合元件内离散随机化的独特序列，将Coop-seq应用于转录因子Sox家族和POU家族的12个二聚体对。该研究揭示了不同Sox因子与Oct4的特定二聚化模式。相比之下，Oct4与三个神经III类POU因子Brn2、Brn4和Oct6与Sox2的组装方式惊人地难以区分。除了已知的复合基序外，两种新的半位点构型也可以支持功能性Sox/Oct二聚化。此外，当间距改变时，Coop-seq揭示了POU半位点内的一个核苷酸开关，这在Sox2/Oct4复合物结合的基因组位点中也有体现。
