Modeling of gap gene regulatory networks in Drosophila with the account of the gene modular structure (in Russian)

TL;DR

This paper presents a modeling approach for gene regulatory networks in Drosophila that accounts for modular cis-regulatory regions and nonlinear transcription kinetics, focusing on the hunchback and Kruppel genes.

Contribution

It introduces a methodology that incorporates gene modularity and nonlinear kinetics to better model complex gene expression patterns in Drosophila.

Findings

Expression patterns are sensitive to input factor variations.

The model captures sharp expression peaks.

Modular regulation influences gene expression dynamics.

Abstract

Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation sites. In particular, sharp expression patterns (peaks or stripes) indicate that gene regulation involves nonlinear transcription factor kinetics (beyond first-order). We propose a methodology for approaching this problem, using the example of the multiple cis-regulatory modules (CRMs) and two transcripts (P1 and P2) found in the Drosophila hunchback (hb) and (CD1 and CD2)in Kruppel (Kr) genes, the genes expressed along the anteroposterior axis of the embryo. The positional characteristics of the mRNA expression patterns are studied for their sensitivity to the variation of the input factors and initial conditions.