A new paper in PNAS, “CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression,” elaborates more functions for supposed “junk DNA” as helping to create functionally relevant structures in DNA. Last year I wrote about non-B DNA (see here and here). It doesn’t necessarily exhibit the typical double-helical DNA structure, but it can form unique shapes that contribute to a variety of important genomic functions. This new paper explores a structure called the G-quadruplex (G4s), a loop shape that often arises in DNA segments rich in guanine. The paper reports that G4s can perform a variety of functions:
G4 binding activities in genomic regulators of nucleosome remodeling, paraspeckle assembly, RNA splicing, and three-dimensional genome organization. Among the prominent hits, we identify the genomic architectural protein, CCCTC-binding factor (CTCF), as one of the strongest G4 binders.
The latter function is crucial, as it reflects the ability of G4 structures to regulate large-scale chromosomal structures:
G-quadruplexes interact with several nuclear protein complexes involved in crucial genomic processes. We found that the genomic architectural protein, CCCTC-binding factor (CTCF), directly binds to G4s and this interaction is important for regulation of genome topology and gene expression. Our work uncovers the architectural roles of G4 structures in the genome and contributes important insights into G4 biology and 3D genome organization.
A Variety of Genomic Functions
Thus, these G4 structures contribute to a variety of genomic functions, and importantly they help form topologically associating domains (TADs) that control the 3D structure of the genome:
At the scale of tens to hundreds of kilobases, the genome is further assembled into self-interacting regions known as topologically associating domains (TADs), with higher propensity of genomic interactions observed within, rather than between TADs. TADs mediate enhancer–promoter interactions and are important for cell-type specific gene expression programs. Interestingly, G4s are shown to be enriched at TAD boundaries and implicated in regulating insulation strength of TADs.
The paper proposes a model that involves “CTCF–G4 interaction in mediating long-range chromatin looping to define stable chromatin loops or boundaries of topologically associating domains (TADs).”
So Why Does This Matter?
A variety of papers note that repetitive DNA — the precise type of DNA that our junk-DNA-defending friends assure us must be functionless — is vital for forming these G4 structures:
- Ambrus et al. (2006): Discusses how telomeric repeats in humans form G-quadruplexes.
- Bryan (2020): Reviews how telomeric repeat DNA forms G-quadruplexes
- Waisertreiger et al. (2025): Discusses how pericentromeric tandem repeat DNA forms G4s.
- Nakagama et al. (2006): Discusses how guanine-rich short tandem repeat DNA forms G4s.
- Zhou et al. (2014): Discusses how the repetitive DNA sequence “GGGGCC” forms G4s.
- Piazza et al. (2017): Explains how minisatellite tandem repeat sequences contribute to G-quadruplex formation.
- Adrian et al. (2014): Shows how a minisatellite repeat sequence forms G4s.
- Raguseo et al. (2023): Explains how the repeat DNA sequence “GGGGCC” forms G4s.
- Bauer et al. (2011): Shows that repetitive telomeric sequences form G4s.
- Geng et al. (2024): Shows G4s are formed by repeat DNA.
These papers demonstrate that various types of repetitive DNA, including in telomeres, minisatellites, pericentromeric repeats, and other tandem repeat DNA sequences, help form G4 structures. The point being: repetitive DNA helps form non-B DNA shapes like G4s, and these G4s are crucial for defining TADs which help define the 3D structure of the genome, regulating gene expression and even defining cell types. Far from being junk, this repetitive DNA is crucial for formatting the genome.
The genome is rich in function, and we dare not simply dismiss any of it.