Deciphering a transcriptional regulatory code: modeling short‐range repression in the Drosophila embryo

Abstract

A well-defined set of transcriptional regulatory modules was created and analyzed in the Drosophila embryo.Fractional occupancy-based models were developed to explain the interaction of short range transcriptional repressors with endogenous activators by using quantitative data from these modules.Our fractional occupancy-based modeling uncovered specific quantitative features of short-range repressors; a complex nonlinear quenching relationship, similar quenching efficiencies for different activators, and modest levels of cooperativityThe extension of the study to endogenous enhancers highlighted several features of enhancer architecture design in Drosophila embryos.

A conserved role for Snail as a potentiator of active transcription

“…GENES & DEVELOPMENT Cold Spring Harbor Laboratory Press on May 8, 2018 -Published by genesdev.cshlp.org Downloaded from Fakhouri et al 2010). The longer spacing between Snail and Twist sites in activated CRMs (50-80 bp) also suggests that there is not a direct close physical interaction between Twist and Snail, which typically occurs when motifs are spaced in the range of 10 bp (for review, see Spitz and Furlong 2012).…”

Investigating giant (Gt) repression in the formation of partially overlapping pair‐rule stripes

“…For Gt, it was shown that in addition to the number of sites and the binding site affinity, the distance between sites and the activator-repressor stoichiometry are also properties that affect Gt repression (Hewitt et al, 1999;Kulkarni and Arnosti, 2005;Fakhouri et al, 2010). According to our bioinformatics analysis, we also verified that number, affinity, and average distance between predicted Gt sites seem to be important properties for Gt repression of h 5, eve 5, run 5, and ftz 5 when compared to predicted Gt sites in other regions in the locus (data not shown; Fig.7).…”

Optimization of reporter gene architecture for quantitative measurements of gene expression in the Drosophila embryo

“…For comparison of promoter and UTR elements, we employed a common 165 bp enhancer containing four Dorsal, four Twist and two Knirps binding sites, 9 which was synthesized using overlapping oligos and cloned into BamHI and EcoRI sites of pattB vector. 1 The enhancer sequence is: 5'-ACC GGT GGG AAA ACC CAA AAT CGA GGG ATT TTC CCA TCT AGA CAT ATG CTC AAC ATA TGG GAT CCC TGA TCT AGT TTG TAC TAG ACA TCT GAT CTA GTT TGG ATC CCA TAT GTT GAG CAT ATG TCT AGA GGG ATT TTC CCA AAT CGA GGG AAA ACC CAA GGC CGG CC-3'.…”

“…2). The transposase promoter has been used extensively in enhancer studies and also in quantitative studies of gene expression; 8,9 this element contains a TATA box. The widely used hsp70 promoter and the PCNA promoter contain a TATA box and Initiator (Inr) motif involved in TFIID interactions.…”

“…Immunofluorescent in situ hybridization and confocal laser scanning microscopy was done as previously described and was done in parallel. 9 Heterozygous embryos with only one copy of transgene were collected for in situ hybridization. Image analysis was done with ImageJ.…”