An interaction network of RNA-binding proteins involved in Drosophila oogenesis

Prashali Bansal; Johannes Madlung; Kristina Schaaf; Boris Macek; Fulvia Bono

Out of 90 protein-protein interactions assayed, we could confirm 32 interactions (35%), of which 26 were found to be novel (summarized in Fig. S6a ). All positive interactions were confirmed at least 3 times, in independent experiments. In addition, we were also able to validate some of the interactions by reciprocal IP, as shown in Fig. 7i . To further confirm that our MS analysis pipeline effectively separated background binders from true interactants, we also tested Nucleophosmin (Nph), which was depleted in all IP-MS datasets. We could not detect interactions of Nph with any of the 4 baits tested in vitro (data not shown), in line with the MS data. Additionally, we also tested Sqd that has been reported to interact with Hrp48 in an RNA-dependent manner (47). The negative results further confirm that our experimental conditions effectively disrupted RNA-mediated associations and only protein-protein interactions were confidently identified in our analyses. To visualize the co-IP results, we integrated the validated interactions with the IP-MS data (both labeled and label-free) and information from the literature to create a subnetwork (Fig. S6b) . As the majority . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.08.899146 doi: bioRxiv preprint of the validated interactants are known regulators of maternal mRNAs, this subnetwork highlights a general machinery involved in oocyte development in Drosophila.