New Preprint on ALC1
Something really cool happened to me this year.
It all started with getting a travel grant to attend this year’s CCP-EM Spring Symposium. It was already cool because I have been eager to attend this conference for a long time now. I watched the online talks when the conference became online-only during the pandemic, and after that when it remained hybrid.
So I traveled to Nottingham in April, right after doing a loop through France to see family over Easter weekend. As expected, the conference was excellent, and it was great to finally experience all the parts that can’t happen online. One of these was the poster session. While browsing posters, I found one that showed a structure looking very familiar. No wonder, since it was from my own previous work! The poster was from Hannah Bridges, an application scientist at Structura Biotechnology, the company making CryoSPARC (an image processing software used to analyze cryo-EM data).
So I made sure to chat with Hannah during one of the poster sessions or coffee breaks. The poster showed a re-analysis of the dataset EMPIAR-10739 from which we had originally solved this structure of ALC1 bound to a PARylated nucleosome, with greatly improved results. I first learned that the main goal of this was to write a case study for the CryoSPARC Guide. One of my structures featured in CryoSPARC’s documentation: how cool is that?! The case study is now online here. If you follow it, re-process this dataset, and find new things that don’t look like the published structures, please do reach out to me! Either privately or in this discussion on the CryoSPARC forum.
It was impressive to see such improvement, given the struggle the initial analysis had turned out to be back in 2021. This dataset is very heterogeneous: getting good reconstructions required a lot of classification, and the whole thing was generally quite challenging. During our discussion, Hannah mentioned that she found another structure in this dataset that refined to sufficient resolution to assign domains. This piqued my curiosity because ALC1 is very dynamic, and none of the nucleosome-bound structures determined so far could resolve its regulatory domain. So if there was any chance of finding this domain, we had to take a closer look at her findings!
Some time after the conference, Hannah sent me the reconstructions she had. It turned out that one of them is most likely an intermediate state of ALC1, somewhere between its auto-inhibited state and its active state tightly bound to the nucleosome. The resolution is only sufficient to assign domains, but the regulatory (macro) domain is definitely visible in this structure! And, cherry on top, this intermediate state clearly makes an interaction with the nucleosome’s super-groove. The super-groove is a structural feature of the nucleosome that has been hypothesized to be recognized by chromatin-binding factors ever since synthetic super-groove binders were designed in the early 2000s (doi:10.1073/pnas.0401743101 ). Turns out this structure is only the second example of such a protein! The other one was published earlier this year by the group of Cynthia Wolberger (PDB 9B2S , EMD-44113 , doi:10.1038/s41594-025-01502-y ). So this is cool again! This time, doubly so: a new structure filling the remaining gap in our understanding of how ALC1 is activated, and confirming a mode of recognition to the nucleosome that so far had only been seen twice (only once with a naturally occurring protein).
I could show some visuals here, but we wrote a preprint about this new structure and there is not much point re-writing it into a blog post. So here are the links to the preprint and structure instead, check them out!
Bridges HR, Bacic L, Deindl S & Gaullier G (2025) ALC1 Finds a New Foothold on the Nucleosome’s Super-Groove. bioRxiv 2025.11.10.687450. doi:10.1101/2025.11.10.687450
This preprint has been a side project from its beginning, since I no longer work on this. I will now do my best to get it peer-reviewed, but I am already very happy with how this all turned out, and the outcome with peer-review will not change that.