GSBS Student Publications


Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping

Student Author(s)

H. Efsun Arda; Christian A. Grove

GSBS Program

Interdisciplinary Graduate Program

UMMS Affiliation

Program in Gene Function and Expression; Program in Molecular Medicine



Document Type


Medical Subject Headings

Animals; Caenorhabditis elegans; *Transcription, Genetic; Two-Hybrid System Techniques


Genetics and Genomics | Life Sciences | Medicine and Health Sciences


Yeast one-hybrid (Y1H) assays provide a gene-centered method for the identification of interactions between gene promoters and regulatory transcription factors (TFs). To date, Y1H assays have involved library screens that are relatively expensive and laborious. We present two Y1H strategies that allow immediate prey identification: matrix assays that use an array of 755 individual Caenorhabditis elegans TFs, and smart-pool assays that use TF multiplexing. Both strategies simplify the Y1H pipeline and reduce the cost of protein-DNA interaction identification. We used a Steiner triple system (STS) to create smart pools of 4-25 TFs. Notably, we uniplexed a small number of highly connected TFs to allow efficient assay deconvolution. Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well.

Rights and Permissions

Citation: Nat Methods. 2007 Aug;4(8):659-64. Epub 2007 Jun 24. Link to article on publisher's site

DOI of Published Version


Related Resources

Link to Article in PubMed

Journal Title

Nature methods

PubMed ID