Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains | Flicek Lab | Institute for Systems Genomics

E Kentepozidou, SJ Aitken, C Feig, K Stefflova, X Ibarra-Soria, DT Odom, M Roller, P Flicek. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biol 2020;21(1):5. doi:10.1186/s13059-019-1894-x
[BibTeX] [Abstract]

BACKGROUND: CTCF 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. RESULTS: We 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. CONCLUSIONS: Dynamic 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.

@Article{31910870,
author = {Kentepozidou E and Aitken SJ and Feig C and Stefflova K and Ibarra-Soria X and Odom DT and Roller M and Flicek P},
title = {Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains},
journal = {Genome Biol},
volume = {21},
number = {1},
pages = {5},
year = {2020},
doi = {10.1186/s13059-019-1894-x},
note = {First posted as a preprint: 12 June 2019},
abstract = {BACKGROUND: CTCF 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. RESULTS: We 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. CONCLUSIONS: Dynamic 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.},}

Description

CTCF 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.

We 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.

Dynamic 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.

Full details are available in the manuscript published in Genome Biology and the preprint submitted to BioRxiv .

Raw Data

All ChIP-seq and RNA-seq data generated in this study are available in the Array Express repository under the accession numbers E-MTAB-8014 , E-MTAB-8471 , and E-MTAB-8016 . Additional ChIP-seq and RNA-seq data that were reused in the study are available under the accession numbers E-MTAB-5769 , E-MTAB-1091 and E-MTAB-2483 .

Hi-C-derived TADs were retrieved from Table S1. Genomic Regions of Interest in: Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture . Cell Rep. 2015;10:1297–309 .

Transposable elements were retrieved from the supplementary page accompanying Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, et al. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res. 2018;28:448–59.

Conserved CTCF binding sites

The results of the cross-species comparisons of CTCF binding conservation, centred on the mm10 genome, can be found here . Column descriptions:

CBS_ID	Unique ID
coord_on_mmus	Genome coordinates on the mm10 genome
m_musculus, m_castaneus, m_spretus, m_caroli, m_pahari	These columns take values [0\|1\|2]. 0 –> The site does not have any orthologous alignment on the genome of the corresponding species. 1–> the site has an orthologous alignment on the genome of the corresponding species, but is not bound by CTCF. 2 –> The site has an orthologous alignment on the genome of the corresponding species and is also bound by CTCF in the corresponding species (validated with ChIP-seq data from the corresponding species).
Cons_Score	Number of species the site is conserved in (has orthologous alignment AND is bound by CTCF)
Align_Score	Number of species with orthologous alignment but is NOT bound by CTCF

To find the genome coordinates of CTCF sites projected to all of the mouse species, a similar file exists here . It has all the columns of the above table, and additionally also coordinate columns corresponding to the orthologous alignment of every site on the genome of each of the other species ( mmus, mcas, mspr, mcar and mpah ).