Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

Elissavet Kentepozidou,Christine Feig,Paul Flicek,Ximena Ibarra-Soria,Maša Roller,Klara Stefflova,Sarah J Aitken,Duncan T Odom

doi:10.1186/s13059-019-1894-x

Abstract

BackgroundCTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive.ResultsWe carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation.ConclusionsDynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.

Highlights

CCCTC binding factor (CTCF) binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs)
Mus-conserved CTCF binding sites commonly occur at TAD borders To investigate the evolution of CTCF binding with respect to the boundaries of topologically associating domains (TADs), we experimentally identified CTCF enriched regions in the livers of 5 Mus species: Mus musculus domesticus (C57BL/6J), M. musculus castaneus (CAST), M. spretus, M. caroli, and M. pahari (Fig. 1a, Additional file 1: Figure S1)
We found that TAD boundary regions with at least one 5-way conserved CTCF site contained a higher number of CTCF sites overall (Fig. 4d) that mainly belong to clusters (Fig. 4e)

Summary

Introduction

CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). A loop extrusion mechanism of TAD formation has been proposed wherein the cohesin protein complex slides along chromatin forming a growing loop until it meets two CTCF molecules bound with convergent orientation. This architecture prevents cohesin from sliding further, demarcating the TAD boundaries [21, 22]. There are ubiquitous CTCF-bound regions with diverse functions throughout the genome, while only a small fraction of them occur at TAD boundaries [4] This has made it challenging to delineate the precise role of CTCF binding in establishing and stabilizing TAD structures

Objectives

Methods

Results

Discussion

Conclusion