Single base-pair resolution analysis of DNA binding motif with MoMotif reveals an oncogenic function of CTCF zinc-finger 1 mutation

Abstract

Defining the impact of missense mutations on the recognition of DNA motifs is highly dependent on bioinformatic tools that define DNA binding elements. However, classical motif analysis tools remain limited in their capacity to identify subtle changes in complex binding motifs between distinct conditions. To overcome this limitation, we developed a new tool, MoMotif, that facilitates a sensitive identification, at the single base-pair resolution, of complex, or subtle, alterations to core binding motifs, discerned from ChIP-seq data. We employed MoMotif to define the previously uncharacterized recognition motif of CTCF zinc-finger 1 (ZF1), and to further define the impact of CTCF ZF1 mutation on its association with chromatin. Mutations of CTCF ZF1 are exclusive to breast cancer and are associated with metastasis and therapeutic resistance, but the underlying mechanisms are unclear. Using MoMotif, we identified an extension of the CTCF core binding motif, necessitating a functional ZF1 to bind appropriately. Using a combination of ChIP-Seq and RNA-Seq, we discover that the inability to bind this extended motif drives an altered transcriptional program associated with the oncogenic phenotypes observed clinically. Our study demonstrates that MoMotif is a powerful new tool for comparative ChIP-seq analysis and characterising DNA-protein contacts.

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation

“…They also identified the identical flanking sequences associated with del1 and del 10, as described in our study [ 50 ]. Of note, while our manuscript was under peer review, a similar study that utilized the ZF1 mutant knockin MCF7 cell line identified the same conserved G associated with ZF1 binding in CTCF’s binding motif identified in this study [ 51 ]. Their data, which was highly consistent with ours, supports and strengthens our findings, since independent approaches were used in each study.…”

A negatively-charged region within carboxy-terminal domain maintains proper CTCF DNA binding

“…16,[30][31][32] Recently, several lines of evidence suggest that ZF1 and ZF2 recognize base pairs downstream of the CTCF core motif. [33][34][35][36][37] Remarkably, CTCF also interacts with RNA to mediate chromatin loop formation and to regulate gene expression pattern. 38,39 Finally, the intrinsically disordered NTD, but not CTD, of CTCF interacts with cohesin complex to anchor chromatin loops between distant DNA elements.…”