Clustering of Drosophila housekeeping promoters facilitates their expression

Abstract

Housekeeping genes of animal genomes cluster in the same chromosomal regions. It has long been suggested that this organization contributes to their steady expression across all the tissues of the organism. Here, we show that the activity of Drosophila housekeeping gene promoters depends on the expression of their neighbors. By measuring the expression of ∼85,000 reporters integrated in Kc167 cells, we identified the best predictors of expression as chromosomal contacts with the promoters and terminators of active genes. Surprisingly, the chromatin composition at the insertion site and the contacts with enhancers were less informative. These results are substantiated by the existence of genomic "paradoxical" domains, rich in euchromatic features and enhancers, but where the reporters are expressed at low level, concomitant with a deficit of interactions with promoters and terminators. This indicates that the proper function of housekeeping genes relies not on contacts with long distance enhancers but on spatial clustering. Overall, our results suggest that spatial proximity between genes increases their expression and that the linear architecture of the Drosophila genome contributes to this effect.

Strand asymmetry influences mismatch resolution during single-strand annealing

“…A TRIP assay to measure mismatch repair biases in SSA TRIP (Thousands of Reporters Integrated in Parallel) is a shotgun technique to assay the influence of the chromatin context on a phenomenon of interest (Akhtar et al . 2013;Corrales et al . 2017;Gisler et al .…”

“…FF fragments (each with a precursor for one of heteromismatches) were synthesised by Life Technologies, and cloned into plasmid pT2 using Gibson Assembly Cloning Kit (NEB, E5510S). Obtained pT2_FF plasmids were used as templates for PCR-based barcoded library preparation (Corrales et al . 2017) .…”

Loci specific epigenetic drug sensitivity

“…Insertion of reporters potentially change the pre-existing epigenetic landscape or cause sequence-specific or protein-specific interactions between regional chromatin and synthetic ORF. However, previous studies suggest that integrated reporters generally do not perturb the chromatin landscape but adopt the local chromatin state [10,75] . Complex sequence-or protein-specific interactions between local chromatin and synthetic reporters were not observed in previous study as well [11] .…”

Evolution of theD. melanogasterchromatin landscape and its associated proteins

“…In Drosophila, housekeeping genes (in YELLOW) have few, relatively short introns, and developmental genes (mostly in RED) start with long 5' introns and have short ones at the 3' end (Corrales et al 2017). We wondered if genes with long 5' introns mostly date to the origin of multicellularity, and if this feature is also found among other multicellular organisms.…”

“…(Lewis 1978;Duncan 1982;Boyer et al 2006;Lee et al 2006;Nègre et al 2006). Finally, BLACK was originally interpreted as a major repressive chromatin type, but recent findings indicate it is better described as a near-neutral type (Filion et al 2010;Corrales et al 2017).…”