Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure. Issue 9 (2nd September 2019)

• Record Type: Journal Article
• Authors: Hou, Yue; Li, Fuyu; Zhang, Rongxin; Li, Sheng; Liu, Hongde; Qin, Zhaohui S.; Sun, Xiao
• Is Part Of: Epigenetics. Volume 14:Issue 9(2019)
• Page Start: 894
• Page End: 911
• Publication Date: 2019-09-02
• Subjects: Chromatin structure -- enhancer-promoter interaction -- G-quadruplex -- Hi-C -- loop extrusion -- transcription factor; Epigenesis -- Periodicals; Epigenetica; 572.86505
• DOI: 10.1080/15592294.2019.1621140
• Languages: English
• ISSNs: 1559-2294

Abstract

ABSTRACT: DNA molecules are highly compacted in the eukaryotic nucleus where distal regulatory elements reach their targets through three-dimensional chromosomal interactions. G-quadruplexes, stable four-stranded non-canonical DNA structures, can change local chromatin organization through the exclusion of nucleosomes. However, the relationship between G-quadruplexes and higher-order genome organization remains unknown. Here, we found that G-quadruplexes are significantly enriched at boundaries of topological associated domains (TADs). Architectural protein occupancy, which plays critical roles in the formation of TADs, was highly correlated with the content of G-quadruplexes at TAD boundaries. Moreover, adjacent boundaries containing G-quadruplexes frequently interacted with each other because of the high enrichment of architectural protein binding sites. Similar to CCCTC-binding factor (CTCF) binding sites, G-quadruplexes also showed strong insulation ability in the separation of adjacent regions. Additionally, the insulation ability of CTCF binding sites and TAD boundaries was significantly reinforced by G-quadruplexes. Furthermore, G-quadruplex motifs on different strands were associated with the orientation of CTCF binding sites. These findings suggest a potential role for G-quadruplexes in loop extrusion. The enrichment of transcription factor binding sites (TFBSs) around regulatory elements containing G-quadruplexes led to frequent interactions between regulatory elements containing G-quadruplexes. Intriguingly, more than 99% of G-quadruplexes overlapped with TFBSs. The binding sites of CTCF and cohesin proteins were preferentially located surrounding G-quadruplexes. Accordingly, we proposed a new mechanism of long-distance gene regulation in which G-quadruplexes are involved in distal interactions between enhancers and promoters.