Efficient learning of discrete graphical models*

Graphical models are useful tools for describing structured high-dimensional probability distributions. Development of efficient algorithms for learning graphical models with least amount of data remains an active research topic. Reconstruction of graphical models that describe the statistics of discrete variables is a particularly challenging problem, for which the maximum likelihood approach is intractable. In this work, we provide the first sample-efficient method based on the interaction screening framework that allows one to provably learn fully general discrete factor models with node-specific discrete alphabets and multi-body interactions, specified in an arbitrary basis. We identify a single condition related to model parametrization that leads to rigorous guarantees on the recovery of model structure and parameters in any error norm, and is readily verifiable for a large class of models. Importantly, our bounds make explicit distinction between parameters that are proper to the model and priors used as an input to the algorithm. Finally, we show that the interaction screening framework includes all models previously considered in the literature as special cases, and for which our analysis shows a systematic improvement in sample complexity.

SNX27-driven membrane localisation of OTULIN antagonises linear ubiquitination and NF-κB signalling activation

Background Linear ubiquitination is a novel type of ubiquitination that plays important physiological roles in signalling pathways such as tumour necrosis factor (TNF) signalling. However, little is known about the regulatory mechanisms of linear ubiquitination, except the well-described enzymatic regulators E3 ligase linear ubiquitin chain assembly complex (LUBAC) and deubiquitinase OTULIN. Results Previously, we identified SNX27, a member of the sorting nexin family protein, as a selective linear ubiquitin chain interactor in mass spectrometry-based ubiquitin interaction screening. Here, we demonstrated that the interaction between the linear ubiquitin chain and SNX27 is mediated by the OTULIN. Furthermore, we found that SNX27 inhibits LUBAC-mediated linear ubiquitin chain formation and TNFα-induced signalling activation. Mechanistic studies showed that, upon TNFα stimulation, OTULIN-SNX27 is localised to membrane-associated TNF receptor complex, where OTULIN deubiquitinates the linear polyubiquitin chain that formed by the LUBAC complex. Significantly, chemical inhibition of SNX27-retromer translocation by cholera toxin inhibits OTULIN membrane localization. Conclusions In conclusion, our study demonstrated that SNX27 inhibits TNFα induced NF-κB signalling activation via facilitating OTULIN to localize to TNF receptor complex.

The interaction between Tu-Izumo1 and Tu-JUNO is involved in turtles hybridization

The specificity of sperm-egg recognition is crucial to species independence, and two proteins (Izumo1 and JUNO) are essential for gamete adhesion/fusion in mammals. However, hybridization, which is very common in turtles, also requires specific recognition of sperm-egg binding proteins. In this study, we discovered that natural selection plays an important role in the codon usage bias of Tu-Izumo1 and Tu-JUNO. Positively selected sites and co-evolutionary analyses between Tu-Izumo1 and Tu-JUNO has been previously reported, and we confirm these results in a larger analysis containing 25 turtle species. We also showed that Tu-JUNO is expressed on the oocyte surface and that Tu-Izumo1 and Tu-JUNO interact with each other directly in different species hybridization combinations. Co-immunization assays revealed that this interaction is evolutionarily conserved in turtles. The results of avidity-based extracellular interaction screening between Tu-Izumo1 and Tu-JUNO for sperm-oocyte binding pairs (both within and across species) likely suggest that the interaction force between Izumo1 and JUNO has a certain correlation in whether the turtles can hybridize. Our results lay a theoretical foundation for the subsequent development of techniques to detect whether different turtle species can interbreed, which would provide the molecular basis for breeding management and species protection of turtles.

The influence of Coulomb interaction screening on the excitons in disordered two-dimensional insulators

We study the joint effect of disorder and Coulomb interaction screening on the exciton spectra in two-dimensional (2D) structures. These can be van der Waals structures or heterostructures of organic (polymeric) semiconductors as well as inorganic substances like transition metal dichalcogenides. We consider 2D screened hydrogenic problem with Rytova–Keldysh interaction by means of so-called fractional Scrödinger equation. Our main finding is that above synergy between screening and disorder either destroys the exciton (strong screening) or promote the creation of a bound state, leading to its collapse in the extreme case. Our second finding is energy levels crossing, i.e. the degeneracy (with respect to index $$\mu $$ μ ) of the exciton eigenenergies at certain discrete value of screening radius. Latter effects may also be related to the quantum manifestations of chaotic exciton behavior in above 2D semiconductor structures. Hence, they should be considered in device applications, where the interplay between dielectric screening and disorder is important.

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation

SummaryCells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. The binding of the TCR-specific repair factor CSB triggers DNA damage-induced ubiquitylation of RNA polymerase II (RNAPII) at a single lysine (K1268) by the CRL4CSA ubiquitin ligase. However, how the CRL4CSA ligase is specifically directed toward the K1268 site is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to the K1268 site, revealing ELOF1 as a specificity factor that positions CRL4CSA for optimal RNAPII ubiquitylation. Furthermore, drug-genetic interaction screening reveals an unanticipated compensatory TCR pathway in which ELOF1 together with known factors DOT1L and HIRA protect CSB-deficient cells from collisions between transcription and replication machineries. Our study provides a genetic framework of the transcription stress response and reveals key insights into the molecular mechanism of TCR.