Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales-Berjano1,
- Aranzazu Rosado Diez1,
- Ruggero Cortini1,
- Joris van Arensbergen2,
- Bas van Steensel2 and
- Guillaume J Filion1,3
- ↵* Corresponding author; email: guillaume.filion{at}gmail.com
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 neighbours. 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.
- Received June 15, 2016.
- Accepted April 12, 2017.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
