A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

摘要: Deciphering the structure of gene regulatory networks across tree life remains one major challenges in postgenomic biology. We present a novel ChIP-seq workflow for archaea using model organism Halobacterium salinarum sp. NRC-1 and demonstrate its application mapping genome-wide binding sites natively expressed transcription factors. This end-to-end pipeline is first protocol archaea, with methods tools each stage from tagging to data analysis biological discovery. Genome-wide factors many (TfbD) are identified sensitivity, while retaining specificity identification smaller regulons (bacteriorhodopsin-activator protein). Chromosomal target proteins compact epitope facilitates standardized cost-effective that compatible high-throughput immunoprecipitation The Pique package, an open-source bioinformatics method, presented events. Relative ChIP-Chip qPCR, this offers robust catalog protein-DNA events improved spatial resolution significantly decreased cost. While study focuses on H. NRC-1, our can also be adapted use other bacteria basic genetic tools.