Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes

Eddie Rodríguez-Carballo,Asier Ullate-Agote,Lucille Lopez-Delisle,Denis Duboule,Nayuta Yakushiji-Kaminatsui

doi:10.1186/s12915-019-0677-x

Abstract

BackgroundThe spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases, such domains may act as coherent regulatory units, with a global on or off state. By using the HoxD gene cluster, which specifies the topology of the developing limbs via highly orchestrated regulation of gene expression, as a paradigm, we investigated how the arrangement of regulatory domains determines their activity and function.ResultsProximal and distal cells in the developing limb express different levels of Hoxd genes, regulated by flanking 3′ and 5′ TADs, respectively. We characterized the effect of large genomic rearrangements affecting these two TADs, including their fusion into a single chromatin domain. We show that, within a single hybrid TAD, the activation of both proximal and distal limb enhancers globally occurred as when both TADs are intact. However, the activity of the 3′ TAD in distal cells is generally increased in the fused TAD, when compared to wild type where it is silenced. Also, target gene activity in distal cells depends on whether or not these genes had previously responded to proximal enhancers, which determines the presence or absence of H3K27me3 marks. We also show that the polycomb repressive complex 2 is mainly recruited at the Hox gene cluster and can extend its coverage to far-cis regulatory sequences as long as confined to the neighboring TAD structure.ConclusionsWe conclude that antagonistic limb proximal and distal enhancers can exert their specific effects when positioned into the same TAD and in the absence of their genuine target genes. We also conclude that removing these target genes reduced the coverage of a regulatory landscape by chromatin marks associated with silencing, which correlates with its prolonged activity in time.

Highlights

The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales
In order to better visualize the spatial distribution of the two Topologically associating domain (TAD) associated with the HoxD cluster (Fig. 1a, b), we modeled their structures in 3D by using Hi-C matrices [34] for both distal and proximal E12.5 limb bud cells (Fig. 1c) and the TADkit scripts package as a 3D modeling viewer [36]
The dashed rectangle illustrates the deletion in the del(attP-Rel5)d9lac allele. c Three-dimensional modeling of HoxD-associated TADs derived from Hi-C datasets obtained from wild-type (Wt) proximal and distal limb bud cells. d Hi-C map showing the extent of the fused-TAD upon deletion of the HoxD locus in proximal limb cells, as well as the remaining genes and regulatory regions. e Comparative modeling from the del(attP-Rel5)d9lacmutant proximal and distal limb bud cells

Summary

Introduction

The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). At the level of gene regulation, topologically associating domains (TADs) [7,8,9] usually match large domains of long-range gene regulation referred to as regulatory landscapes [10] These structures are globally detected in all cell types and conserved across vertebrate species [7, 11,12,13,14,15]. The experimental depletion of either CTCF or cohesin subunits leads to a loss of both loop organization and TAD structure Under these conditions, the effects upon gene transcription were limited and the formation of larger structures (compartments), which may be functionally relevant, still occurred in an altered manner [16,17,18,19,20]

Methods

Results

Discussion

Conclusion