CTCF Binding Polarity Determines Chromatin Looping

TY - JOUR

T1 - CTCF Binding Polarity Determines Chromatin Looping

AU - de Wit, Elzo

AU - Vos, Erica S M

AU - Holwerda, Sjoerd J B

AU - Valdes-Quezada, Christian

AU - Verstegen, Marjon J A M

AU - Teunissen, Hans

AU - Splinter, Erik

AU - Wijchers, Patrick J

AU - Krijger, Peter H L

AU - de Laat, Wouter

N1 - Copyright © 2015 Elsevier Inc. All rights reserved.

PY - 2015/10/27

Y1 - 2015/10/27

N2 - CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR/Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal, convergent CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher-order chromatin structure.

AB - CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR/Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal, convergent CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher-order chromatin structure.

U2 - 10.1016/j.molcel.2015.09.023

DO - 10.1016/j.molcel.2015.09.023

M3 - Article

C2 - 26527277

SN - 1097-2765

JO - Molecular Cell

JF - Molecular Cell

ER -