Please check out our new paper showing that the supposed looping factor ZNF143 has no role in chromatin looping: www.cell.com/molecular-ce... And also check out the companion paper from @andersshansen.bsky.social: www.cell.com/molecular-ce... - ThreadSky

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dewitlab.bsky.social • 68 days ago

Please check out our new paper showing that the supposed looping factor ZNF143 has no role in chromatin looping: https://www.cell.com/molecular-cell/fulltext/S1097-2765(24)00956-0

And also check out the companion paper from @andersshansen.bsky.social: https://www.cell.com/molecular-cell/fulltext/S1097-2765(24)00957-2

Comments

dewitlab.bsky.social•68 days ago

This is the version of record for our pre-print: https://www.biorxiv.org/content/10.1101/2024.03.08.583864v1

dewitlab.bsky.social•68 days ago

We performed degron experiments for ZFP143 (mouse ZNF143) and could not detect any changes in the Hi-C maps, suggesting that this protein might have nothing to do with looping.

dewitlab.bsky.social•68 days ago

Why then are there so many papers suggesting the opposite? It turns out that one widely used antibody (used also by the ENCODE consortium) also detects binding at CTCF sites. Other antibodies (and our ZNF143-HA tagged ChIPseq experiments) did not detect binding at CTCF sites.

dewitlab.bsky.social•68 days ago

This smells like antibody cross-reactivity. To confirm this we contacted @guertin.bsky.social who used the cross-reacting antibody to ChIP ZNF143 in the absence in absence of ZNF143.

dewitlab.bsky.social•68 days ago

While the “real” ZNF143 peaks are diminished, those overlapping with CTCF binding sites are increased, which is exactly what you would expect in the absence of the primary antibody target.

dewitlab.bsky.social•68 days ago

Our results mean it is very unlikely that ZFP143 is a general looping factor like CTCF as is suggested by a lot of literature. So what is it doing?

guertin.bsky.social•68 days ago

congratulations! great to see the record corrected, although these things are always anticlimatic because you and Anders convinced me a year ago in the preprints!

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