Talks

Based on the immense popularity of causal Bayesian networks and structural causal models, one might expect that these representations are appropriate to describe the causal semantics of any real-world system, at least in principle. In this talk, I will argue that this is not the case, and motivate the study of more general causal modeling frameworks. In particular, I will discuss bipartite graphical causal models. Real-world complex systems are often modelled by systems of equations with endogenous and independent exogenous random variables. Such models have a long tradition in physics and engineering. The structure of such systems of equations can be encoded by a bipartite graph, with variable and equation nodes that are adjacent if a variable appears in an equation. I will show how one can use Simon’s causal ordering algorithm and the Dulmage-Mendelsohn decomposition to derive a Markov property that states the conditional independence for (distributions of) solutions of the equations in terms of the bipartite graph. I will then show how this Markov property gives rise to a do-calculus for bipartite graphical causal models, providing these with a refined causal interpretation.

In the Statistics literature there are three main frameworks for causal modeling: counterfactuals (aka potential outcomes), non-parametric structural equation models (NPSEMs) and graphs (aka path diagrams or causal Bayes nets). These approaches are similar and, in certain specific respects, equivalent. However, there are important conceptual differences and each formulation has its own strengths and weaknesses. These divergences are of relevance both in theory and when the approaches are applied in practice. This talk will introduce the different frameworks, and describe, through examples, both the commonalities and dissimilarities. In particular, we will see that the “default” assumptions within these frameworks lead to different identification results when quantifying mediation and, more generally, path-specific effects.

Can the effectiveness of a medical treatment be determined without the expense of a randomized controlled trial? Can the impact of a new policy be disentangled from other factors that happen to vary at the same time? Questions such as these are the purview of the field of causal inference, a general-purpose science of cause and effect, applicable in domains ranging from epidemiology to economics. Researchers in this field seek in particular to find techniques for extracting causal conclusions from statistical data. Meanwhile, one of the most significant results in the foundations of quantum theory—Bell’s theorem—can also be understood as an attempt to disentangle correlation and causation. Recently, it has been recognized that Bell’s result is an early foray into the field of causal inference and that the insights derived from almost 60 years of research on his theorem can supplement and improve upon state-of-the-art causal inference techniques. In the other direction, the conceptual framework developed by causal inference researchers provides a fruitful new perspective on what could possibly count as a satisfactory causal explanation of the quantum correlations observed in Bell experiments. Efforts to elaborate upon these connections have led to an exciting flow of techniques and insights across the disciplinary divide. This tutorial will highlight some of what is happening at the intersection of these two fields.

The DNA-binding protein from starved cells (Dps) plays a crucial role in maintaining bacterial cell viability during periods of stress. Dps is a nucleoid-associated protein that interacts with DNA to create biomolecular condensates in live bacteria. Purified Dps protein can also rapidly form large complexes when combined with DNA in vitro. However, the mechanism that allows these complexes to nucleate on DNA remains unclear. Here, we examine how DNA topology influences the formation of Dps-DNA complexes. We find that DNA supercoils offer the most preferred template for the nucleation of condensed Dps structures. More generally, bridging contacts between different regions of DNA can facilitate the nucleation of condensed Dps structures. In contrast, Dps shows little affinity for stretched linear DNA before it is relaxed. Once DNA is condensed, Dps forms a stable complex that can form inter-strand contacts with nearby DNA, even without free Dps present in solution. Taken together, our re...

The MYC oncogene has been studied for decades, yet there is still intense debate over how this transcription factor controls gene expression. We engineered an optogenetic variant of MYC (Pi-MYC) and combined this tool with single-molecule RNA and protein imaging techniques to investigate the role of MYC in modulating transcriptional bursting and transcription factor binding dynamics in human cells. We find that the mechanism by which MYC exerts global effects on the active period of genes is by altering the binding dynamics of transcription factors involved in RNA Polymerase II complex assembly and productive elongation. These studies expose fundamental questions about transcription regulation. Namely, how do transient interactions (~ seconds) between transcription factors and promoters lead to specific responses? We propose an extension of kinetic proofreading to explain transcriptional regulation in eukaryotes. This model suggests active, ATP-consuming processes drive transcription f...

In higher eukaryotic cells, strings of nucleosomes, where long genomic DNA is wrapped around core histones, are irregularly folded into numerous condensed chromatin domains (1,2). Inside these domains, nucleosomes fluctuate and locally behave like a liquid (2,3). While nucleosome behavior is assumed to be highly related to genome functions, it remains unclear how this behavior changes during the cell cycle. During interphase, the nucleus enlarges and genomic DNA doubles. Previous reports have shown that chromatin movements vary during interphase on a minute or longer time-scale. However, using single-nucleosome imaging and tracking (4), we reveal that local nucleosome motion on a second time-scale remains steady throughout the G1, S, and G2 phases in live human cells (4). Combined with Brownian dynamics modeling, our results suggest that this steady-state nucleosome motion is mainly driven by thermal fluctuations. We propose that this observed steady-state nucleosome motion allows cell...

The location of nucleosomes in DNA and their structural stability are critical in regulating DNA compaction, site accessibility, and epigenetic gene regulation. Here, we combine the nanopore platform-based fast and label-free single-molecule detection technique with a voltage-dependent force rupture assay to detect distinct structures on nucleosomal arrays and then to induce breakdown of individual nucleosome complexes. Specifically, we demonstrate direct measurement of distinct nucleosome structures present on individual 12-mer arrays. A detailed event analysis showed that nucleosomes are present as a combination of complete and partial structures, during translocation through the pore. By comparing with the voltage-dependent translocation of the mononucleosomes, we find that the partial nucleosomes result from voltage-dependent structural disintegration of nucleosomes. High signal-to-noise detection of heterogeneous levels in translocation of 12-mer array molecules quantifies the het...