Biology
Document Type
Article
Abstract
Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-kB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships between repressor and activator binding sites. Importantly, the collective predictions of sets of models were effective at novel enhancer identification and characterization. Our study demonstrates how experimental dataset and modeling can be effectively combined to provide quantitative insights into cis-regulatory information on a genome-wide scale.
Publication Title
eLife
Publication Date
5-6-2016
Volume
5
Issue
MAY2016
ISSN
2050-084X
DOI
10.7554/eLife.08445
Keywords
gene expression regulation, Drosophila, genetics, enhancer activity
Repository Citation
Sayal, Rupinder; Dresch, Jacqueline M.; Pushel, Irina; Taylor, Benjamin R.; and Arnosti, David N., "Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo" (2016). Biology. 120.
https://commons.clarku.edu/faculty_biology/120
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright Conditions
Sayal, R., Dresch, J. M., Pushel, I., Taylor, B. R., & Arnosti, D. N. (2016). Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo. Elife, 5, e08445.
