Wednesday, July 2, 2025

What are all the proteins with direct access to DNA?

 


I  just stumbled on this one while trying to find the PI's email to ask questions about previous studies and online resources from his group - and then I had to send this out to all my DNA researching friends.


Wait. We know what protein has direct access to all the DNA, right? It's histones! I can find you 400 nice little sketches right now and can generate a bunch of figures on BioRender that clearly show DNA is wrapped up in Histones 1-4 (with random letters and numbers and the occasional dashes). And that's all the proteins around until everything unwinds for transcription.

Aaaaaaaaaaaaaaaaaaaaaaaaaaaannnnnnnnnnnnnnnnnnnnnnnnndddd..... just like everything in biology it is not at all that simple.....

These authors demonstrate a "zero length" crosslinking method catalyzed (? might not be the correct term) by high power UV irradiation. The device may be a custom rig for this study. Then they wash or digest then wash away all the nucleic acid stuff that isn't crosslinked. 

A combination of nucleotide sequencing and LCMS proteomics are then used to analyze what's left. You're here for the latter thing, which is good because it's 4am and I have a deadline today for something that...isn't....blogging.... The proteomics is done by microflow analysis on a Tribrid running high resolution MS1 and MS2, which is good because this is how they needed search their data --


-and as someone who just got off of a 4 year polyADPr adventure bus - you want the drivers to use the highest resolution MS/MS you can find to open search for mods this big successfully.

Gotta run, but here is the punchline. After multiple complex negative controls - and introducing stable isotope amino acid labels for confidence - they find compelling evidence of around 1,000 (!!) proteins directly interacting with DNA!!

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