Insulator function and topological domain border strength scale with architectural protein occupancy

Kevin Van Bortle,Zhaohui S Qin,Victor G Corces,Michael H Nichols,Chin-Tong Ong,Naomi Takenaka,Li Li

doi:10.1186/gb-2014-15-5-r82

Abstract

BackgroundChromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains. The borders of these domains are highly enriched for architectural proteins with characterized roles in insulator function. However, a majority of architectural protein binding sites localize within topological domains, suggesting sites associated with domain borders represent a functionally different subclass of these regulatory elements. How topologically associating domains are established and what differentiates border-associated from non-border architectural protein binding sites remain unanswered questions.ResultsBy mapping the genome-wide target sites for several Drosophila architectural proteins, including previously uncharacterized profiles for TFIIIC and SMC-containing condensin complexes, we uncover an extensive pattern of colocalization in which architectural proteins establish dense clusters at the borders of topological domains. Reporter-based enhancer-blocking insulator activity as well as endogenous domain border strength scale with the occupancy level of architectural protein binding sites, suggesting co-binding by architectural proteins underlies the functional potential of these loci. Analyses in mouse and human stem cells suggest that clustering of architectural proteins is a general feature of genome organization, and conserved architectural protein binding sites may underlie the tissue-invariant nature of topologically associating domains observed in mammals.ConclusionsWe identify a spectrum of architectural protein occupancy that scales with the topological structure of chromosomes and the regulatory potential of these elements. Whereas high occupancy architectural protein binding sites associate with robust partitioning of topologically associating domains and robust insulator function, low occupancy sites appear reserved for gene-specific regulation within topological domains.

Highlights

Chromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains
The relative occupancy of architectural proteins at Architectural protein binding site (APBS) scales with the strength of topologically associating domain (TAD) borders, as well as the capacity of these elements to function as enhancer-blocking insulators in transgenic reporter assays, suggesting the composition of these regulatory elements underlies a spectrum of regulatory potential
Genome-wide analysis confirms the localization of dTFIIIC220 to tRNA genes and sites associated with the TFIIIB complex as expected (Figure 1a-c), and MEME-chromatin immunoprecipitation (ChIP) and CentriMo consensus sequence analysis further demonstrates central motif enrichment for both the Drosophila A box and B box elements in our ChIP-seq experiments (Figure 1d,e) [28,29]. dTFIIIC220 binding sites determined by the commonly used MACS peak calling algorithm [30] are present at a majority of annotated tRNA genes obtained from Flybase (Figure 1f) [31], and dTFIIIC220 reads are significantly enriched over all annotated tRNA genes and TFIIIB subunit (TRF1 and BRF) binding sites (Figure 1b,c)

Summary

Introduction

Chromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains. The borders of these domains are highly enriched for architectural proteins with characterized roles in insulator function. A majority of architectural protein binding sites localize within topological domains, suggesting sites associated with domain borders represent a functionally different subclass of these regulatory elements. How topologically associating domains are established and what differentiates border-associated from non-border architectural protein binding sites remain unanswered questions. To avoid further sustaining this confusion, we hereafter refer to proteins associated with insulator function as architectural proteins, and refer to insulators only in the context of elements capable of enhancer-blocking activity

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Results

Discussion

Conclusion