Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans

Katherine Tian,Jack R Bateman,Alexia Brown,Reyna Parker,Justine E Johnson,Rachel E Henderson,Giovanni Bosco

doi:10.1371/journal.pgen.1008152

Abstract

For many genes, proper gene expression requires coordinated and dynamic interactions between multiple regulatory elements, each of which can either promote or silence transcription. In Drosophila, the complexity of the regulatory landscape is further complicated by the tight physical pairing of homologous chromosomes, which can permit regulatory elements to interact in trans, a phenomenon known as transvection. To better understand how gene expression can be programmed through cis- and trans-regulatory interactions, we analyzed transvection effects for a collection of alleles of the eyes absent (eya) gene. We find that trans-activation of a promoter by the eya eye-specific enhancers is broadly supported in many allelic backgrounds, and that the availability of an enhancer to act in trans can be predicted based on the molecular lesion of an eya allele. Furthermore, by manipulating promoter availability in cis and in trans, we demonstrate that the eye-specific enhancers of eya show plasticity in their promoter preference between two different transcriptional start sites, which depends on promoter competition between the two potential targets. Finally, we show that certain alleles of eya demonstrate pairing-sensitive silencing resulting from trans-interactions between Polycomb Response Elements (PREs), and genetic and genomic data support a general role for PcG proteins in mediating transcriptional silencing at eya. Overall, our data highlight how eya gene regulation relies upon a complex but plastic interplay between multiple enhancers, promoters, and PREs.

Highlights

The eukaryotic genome is rich in regulatory elements whose combined inputs lead to proper execution of programmed patterns of gene expression
Other DNA elements play roles in preventing transcription locally, including Polycomb Response Elements (PREs), which bind to complexes of proteins known as the Polycomb Group (PcG) and can create a silenced chromatin domain via the histone mark H3K27me3 [3, 4]
In Drosophila, specificity of interactions between regulatory sequences is further complicated by the phenomenon of somatic homolog pairing, where homologous chromosomes are held in close proximity in virtually all somatic cells of the organism [5]

Summary

Introduction

The eukaryotic genome is rich in regulatory elements whose combined inputs lead to proper execution of programmed patterns of gene expression. Regulatory elements that promote gene expression include promoters, where RNA polymerases begin transcription of genes, and enhancers, which bind to transcriptional activator proteins and are thought to physically interact with promoters via looping, thereby recruiting or activating RNA polymerases [1, 2]. The term transvection encompasses several types of pairingdependent genetic interactions, including those that positively impact gene expression, as is the case when an enhancer on one chromosome acts in trans to activate transcription from a promoter on the homologous chromosome, or that negatively impact gene expression, as observed in some cases when PREs interact in trans, which is thought to increase the efficacy of PcG proteins bound to the PRE in silencing transcription (Fig 1) [5, 7]

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Results

Discussion

Conclusion