Evaluation of DNA-binding preferences of non-metazoan C2H2 zinc finger proteins by PBM

The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs). Here, we have explored the diversity of sequence preferences of C2H2-ZF proteins in non-metazoan organisms using PBM experiments. Protein binding microarray (PBM) experiments were performed for a set of 43 full-length non-metazoan C2H2-ZF proteins. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

真核转录因子中规模最大、多样性最丰富的类群含有半胱氨酸2-组氨酸2锌指结构（Cys2-His2 zinc fingers，C2H2-ZFs）。本研究借助蛋白质结合微阵列（Protein binding microarray，PBM）实验，系统探究了非后生生物体内C2H2-ZF蛋白的序列偏好多样性。我们针对43种全长非后生生物C2H2-ZF蛋白开展了PBM实验：简言之，该实验将带有谷胱甘肽S-转移酶（GST）标签的DNA结合蛋白与两种双链44K安捷伦（Agilent）微阵列进行结合孵育，这两种微阵列分别搭载不同的德布鲁因（DeBruijn）序列设计，以此测定其序列结合偏好。该PBM实验的详细方案已在Berger等人2006年发表于《自然·生物技术》（Nature Biotechnology）的研究中予以说明。