Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding.

Nuclear proteins bind chromatin to execute and regulate genome-templated processes. While studies of individual nucleosome interactions have suggested that an acidic patch on the nucleosome disk may be a common site for recruitment to chromatin, the pervasiveness of acidic patch binding and whether other nucleosome binding hot-spots exist remain unclear. Here, we use nucleosome affinity proteomics with a library of nucleosomes that disrupts all exposed histone surfaces to comprehensively assess how proteins recognize nucleosomes. We find that the acidic patch and two adjacent surfaces are the primary hot-spots for nucleosome disk interactions, whereas nearly half of the nucleosome disk participates only minimally in protein binding. Our screen defines nucleosome surface requirements of nearly 300 nucleosome interacting proteins implicated in diverse nuclear processes including transcription, DNA damage repair, cell cycle regulation and nuclear architecture. Building from our screen, we demonstrate that the Anaphase-Promoting Complex/Cyclosome directly engages the acidic patch, and we elucidate a redundant mechanism of acidic patch binding by nuclear pore protein ELYS. Overall, our interactome screen illuminates a highly competitive nucleosome binding hub and establishes universal principles of nucleosome recognition.

Developing socio-ecological scenarios: A participatory process for engaging stakeholders.

Deltas are experiencing profound demographic, economic and land use changes and human-induced catchment and climate change. Bangladesh exemplifies these difficulties through multiple climate risks including subsidence/sea-level rise, temperature rise, and changing precipitation patterns, as well as changing management of the Ganges and Brahmaputra catchments. There is a growing population and economy driving numerous more local changes, while dense rural population and poverty remain significant. Identifying appropriate policy and planning responses is extremely difficult in these circumstances. This paper adopts a participatory scenario development process incorporating both socio-economic and biophysical elements across multiple scales and sectors as part of an integrated assessment of ecosystem services and livelihoods in coastal Bangladesh. Rather than simply downscale global perspectives, the analysis was driven by a large and diverse stakeholder group who met with the researchers over four years as the assessment was designed, implemented and applied. There were four main stages: (A) establish meta-framework for the analysis; (B) develop qualitative scenarios of key trends; (C) translate these scenarios into quantitative form for the integrated assessment model analysis; and (D) a review of the model results, which raises new stakeholder insights (e.g., preferred adaptation and policy responses) and questions. Step D can be repeated leading to an iterative learning loop cycle, and the process can potentially be ongoing. The strong and structured process of stakeholder engagement gave strong local ownership of the scenarios and the wider process. This process can be generalised for widespread application across socio-ecological systems following the same four-stage approach. It demands sustained engagement with stakeholders and hence needs to be linked to a long-term research process. However, it facilitates a more credible foundation for planning especially where there are multiple interacting factors.

Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase.

Histone H3 lysine 79 (H3K79) methylation is enriched on actively transcribed genes, and its misregulation is a hallmark of leukemia. Methylation of H3K79, which resides on the structured disk face of the nucleosome, is mediated by the Dot1L methyltransferase. Dot1L activity is part of a trans-histone crosstalk pathway, requiring prior histone H2B ubiquitylation of lysine 120 (H2BK120ub) for optimal activity. However, the molecular details describing both how Dot1L binds to the nucleosome and why Dot1L is activated by H2BK120 ubiquitylation are unknown. Here, we present the cryoelectron microscopy (cryo-EM) structure of Dot1L bound to a nucleosome reconstituted with site-specifically ubiquitylated H2BK120. The structure reveals that Dot1L engages the nucleosome acidic patch using a variant arginine anchor and occupies a conformation poised for methylation. In this conformation, Dot1L and ubiquitin interact directly through complementary hydrophobic surfaces. This study establishes a path to better understand Dot1L function in normal and leukemia cells.