In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

Rodrigo G Arzate-Mejía,Félix Recillas-Targa,Mayra Furlan-Magaril,Angel Josué Cerecedo-Castillo,Georgina Guerrero

doi:10.1038/s41467-020-14651-z

Rodrigo G Arzate-Mejía, Félix Recillas-Targa + Show 3 more

Open Access

https://doi.org/10.1038/s41467-020-14651-z

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Journal: Nature Communications	Publication Date: Feb 14, 2020
Citations: 35	License type: open-access

Affiliation: Universidad Nacional Autónoma de México

Abstract

Chromosomes are organized into high-frequency chromatin interaction domains called topologically associating domains (TADs), which are separated from each other by domain boundaries. The molecular mechanisms responsible for TAD formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by architectural proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence of the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila.

Highlights

Chromosomes are organized into high-frequency chromatin interaction domains called topologically associating domains (TADs), which are separated from each other by domain boundaries
In Drosophila, the bands observed in polytene chromosomes correspond to TADs, and inter-band regions have a close correspondence with TAD boundaries[27,28], which suggest that the Notch locus is a TAD itself and the 5′ intergenic region is a domain boundary
Topological disorganization of the first domain of Notch is accompanied by loss of architectural proteins (APs) and RNA Pol II occupancy at the disrupted boundary, reduction in transcription of the exons that reside within the affected domain and changes in the transcription levels of genes located in adjacent TADs

Summary

Introduction

Chromosomes are organized into high-frequency chromatin interaction domains called topologically associating domains (TADs), which are separated from each other by domain boundaries. Our results provide compelling evidence of the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila. We uncovered that portions of the 5′ intergenic region, with binding sites for specific APs, act as discrete chromatin insulators between the upstream gene kirre and Notch, with removal of all regions necessary for TAD fusion. Topological disorganization of the first domain of Notch is accompanied by loss of APs and RNA Pol II occupancy at the disrupted boundary, reduction in transcription of the exons that reside within the affected domain and changes in the transcription levels of genes located in adjacent TADs. Removal of the intragenic enhancer resulted in the fusion of the two Notch domains and decreased transcription along the locus.

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