I'm surprised that we should be surprised:
beyond 3D genome and open chromatin—it is the DNA Consensus sequence recognition that makes this difference!
Good old transcription factors biology.

And this feature of how Wnt/β-catenin seems to be universal - not only in hepatoblastoma 👇

The mechanistic answer is not far. It is the TCF/LEF diversity that bring β-catenin here or there!

Long story short, β-catenin has different targets in the two cell types 😱

In Hepatoblastoma two subtypes coexist, the fetal (F) more liver-like, and the embryonal (E), less dedifferentiated and more aggressive

In both there is constitutively active β-catenin
How does E cells express more classical #Wnt target genes?

Why this matters?

It shows that extracellular signals (e.g. #WNT) are acute genomic remodellers

The Genome - both sequence and 3D structure - is complex but in a matter of minutes it responds to external clues

This is a beautiful adaptation towards cell plasticity.

Are the CTCF-mediated 3D interactions sites (RUWs) functionally important for #WNT activation ⚒️
Yes.
The evidence?
If individual RUWs are mutated ✂️ they halve (of ~40%) the WNT>induction of ONLY that gene!

We discovered
CTCF/Cohesin Repositioning Under Wnt (RUWs):
✅new CTCF binding sites across the genome in WNT-ON genome-wide
✅RUWs are needed for proper target gene expression
✅Yes, these include the usual suspects (e.g. AXIN2)
✅RUWs are dependent on β-catenin, which interacts with CTCF

This ⬇️ is the @liu.se crew @kawresearch.bsky.social @scilifelab.se
On its way to #PALS2025 in superb Göteborg!

Structure inspection and #AlphaFold prediction uncovered a short Asn-Pro-Phe (NPF) motif that mediates these interactions

NPF deletion abrogates binding to #WNT nuclear complex and ability to enhance WNT transcription - BINGO!🎯

One million 💰 Q: Can we Target TBX3-NPF in human CRC?

Proximity proteomics shows that TBX3 becomes physically proximal to members of the #WNT transcriptional complex, including β-catenin and the SWI/SNF

We made a potpourri of CAGE-seq, CUT&RUN and HiChIP-H3K27ac in CRC cells to identify the transcriptional instances directly regulated by TBX3 + β-catenin
Most targets are genes known regulator of metastasis in human CRC ⬇️

Look where TBX3 is expressed in hCRC > together with AXIN2 and Wnt-related genes in LGR5+ cells (Fig left)

And impressive is the genomic co-occupancy between TBX3 and β-catenin (Fig right)

Surprising was that some regulatory elements are very crowded - we called them POPULAR REGIONS

POP Regions:

- are found in the proximity of essential genes (KO is lethal)
- tend to be more evoutionarily conserved than other elements
- cluster aroud TSSs

In our ICEBERG paper we wrote this (see below) 👇
Do you agree with us?

We are using CUT&RUN-LoV-U to map effectors of Signaling Pathways across tissue and stages of Mouse #DevBio🐭🧬

Do you want to join forces and collaborate to build the future of the TranscriptionFactorBinding(TFB)-OMICS?
www.biorxiv.org/content/10.1...