Gene Regulation: Boundaries within Limits

Abstract

Quantitative measurements of the Hunchback transcription factor in Drosophila embryos show that its target genes can respond with a high degree of precision to the exact level of the protein, simulating a continuous, analog readout, while other target genes show a combinatorial effect, resembling a Boolean logic element.

Dampened regulates the activating potency of Bicoid and the embryonic patterning outcome in Drosophila

“…Specifically, the spacing between the anterior boundaries of even-skipped ( eve ) stripes 3 and 4 (referred to as ΔEL eve3-4 ) is known to be controlled by the absolute Hb concentrations in the embryo 47,48 . A reduction in the absolute Hb level (in hb /+ heterozygous embryos) has a well-documented consequence of enlarging ΔEL eve3-4 47,48 .…”

“…Specifically, the spacing between the anterior boundaries of even-skipped ( eve ) stripes 3 and 4 (referred to as ΔEL eve3-4 ) is known to be controlled by the absolute Hb concentrations in the embryo 47,48 . A reduction in the absolute Hb level (in hb /+ heterozygous embryos) has a well-documented consequence of enlarging ΔEL eve3-4 47,48 . To determine whether the effect of Dmpd on hb transcription (i.e., the reduced amplitude) can be propagated further downstream of the AP patterning network, we performed quantitative FISH to detect eve expression patterns in wt and dmpd embryos for a direct comparison of ΔEL eve3-4 .…”

“…Its importance may be better appreciated from the perspective of regulatory networks that control the patterning outcome. In the case of hb as a direct target gene of Bcd, its encoded protein Hb acts as an input, in a concentration-dependent manner 47,48 , for genes (such as eve ) that are further downstream of the AP patterning network. The regulation of the expression of these downstream genes allows the regulatory network to refine and evolve toward the desired final outcome of patterning.…”

Modulation of temporal dynamics of gene transcription by activator potency in theDrosophilaembryo

“…S7A,B for individual profiles). Here we focused specifically on the distance between the anterior boundaries of eve stripes 3 and 4 (referred to as ΔEL eve3-4 ), a spatial feature known to be directly sensitive to hb gene dose (Payankaulam and Arnosti, 2008;Yu and Small, 2008). We recorded ΔEL eve3-4 values of 10.34±1.59 and 9.07±1.01 ( percentage egg length, mean±s.d.)…”

Taking into account nucleosomes for predicting gene expression

“…However, recent studies have shown that GRFs are also strongly dependent on covalent histone modifications of nucleosomes covering the corresponding region [51]. In some cases GRFs can be defined in the form of Boolean functions of TF concentrations [47,48], linear functions of TF occupancies at their binding sites [8] or mixed "analog" scenarios [52]. Recent studies of well-defined prokaryotic systems showed that in a general case GRFs are neither Boolean, nor linear [4,48,53].…”