Open AccessA yeast one‐hybrid and microfluidics‐based pipeline to map mammalian gene regulatory networks
Author(s) -
Gubelmann Carine,
Waszak Sebastian M,
Isakova Alina,
Holcombe Wiebke,
Hens Korneel,
Iagovitina Antonina,
Feuz JeanDaniel,
Raghav Sunil K,
Simicevic Jovan,
Deplancke Bart
Publication year - 2013
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2013.38
Subject(s) - biology , enhancer , computational biology , regulatory sequence , regulation of gene expression , promoter , gene , gene regulatory network , transcription factor , genetics , cis regulatory module , open reading frame , genomic library , gene expression , base sequence , peptide sequence
The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression by identifying their trans‐ regulatory inputs. Here, we present the generation of a mouse‐specific transcription factor (TF) open‐reading frame clone library and its implementation in yeast one‐hybrid assays to enable large‐scale protein–DNA interaction detection with mouse regulatory elements. Once specific interactions are identified, we then use a microfluidics‐based method to validate and precisely map them within the respective DNA sequences. Using well‐described regulatory elements as well as orphan enhancers, we show that this cross‐platform pipeline characterizes known and uncovers many novel TF–DNA interactions. In addition, we provide evidence that several of these novel interactions are relevant in vivo and aid in elucidating the regulatory architecture of enhancers.