Yeast Smy2 and its human homologs GIGYF1 and -2 regulate Cdc48/VCP function during transcription stress.

The "last resort" pathway results in ubiquitylation and degradation of RNA polymerase II in response to transcription stress and is governed by factors such as Def1 in yeast. Here, we show that the SMY2 gene acts as a multi-copy suppressor of DEF1 deletion and functions at multiple steps of the last resort pathway. We also provide genetic and biochemical evidence from disparate cellular processes that Smy2 works more broadly as a hitherto overlooked regulator of Cdc48 function. Similarly, the Smy2 homologs GIGYF1 and -2 affect the transcription stress response in human cells and regulate the function of the Cdc48 homolog VCP/p97, presently being explored as a target for cancer therapy. Indeed, we show that the apoptosis-inducing effect of VCP inhibitors NMS-873 and CB-5083 is GIGYF1/2 dependent.

Pronounced interplay between intrinsic phase-coexistence and octahedral tilt magnitude in hole-doped lanthanum cuprates.

Definitive understanding of superconductivity and its interplay with structural symmetry in the hole-doped lanthanum cuprates remains elusive. The suppression of superconductivity around 1/8th doping maintains particular focus, often attributed to charge-density waves (CDWs) ordering in the low-temperature tetragonal (LTT) phase. Central to many investigations into this interplay is the thesis that La1.875Ba0.125CuO4 and particularly La1.675Eu0.2Sr0.125CuO4 present model systems of purely LTT structure at low temperature. However, combining single-crystal and high-resolution powder X-ray diffraction, we find these to exhibit significant, intrinsic coexistence of LTT and low-temperature orthorhombic domains, typically associated with superconductivity, even at 10 K. Our two-phase models reveal substantially greater tilting of CuO6 octahedra in the LTT phase, markedly buckling the CuO2 planes. This would couple significantly to band narrowing, potentially indicating a picture of electronically driven phase segregation, reminiscent of optimally doped manganites. These results call for reassessment of many experiments seeking to elucidate structural and electronic interplay at 1/8 doping.

UBAP2/UBAP2L regulate UV-induced ubiquitylation of RNA polymerase II and are the human orthologues of yeast Def1.

During transcription, RNA polymerase II (RNAPII) faces numerous obstacles, including DNA damage, which can lead to stalling or arrest. One mechanism to contend with this situation is ubiquitylation and degradation of the largest RNAPII subunit, RPB1 - the 'last resort' pathway. This conserved, multi-step pathway was first identified in yeast, and the functional human orthologues of all but one protein, RNAPII Degradation Factor 1 (Def1), have been discovered. Here we show that following UV-irradiation, human Ubiquitin-associated protein 2 (UBAP2) or its paralogue UBAP2-like (UBAP2L) are involved in the ubiquitylation and degradation of RNAPII through the recruitment of Elongin-Cul5 ubiquitin ligase. Together, our data indicate that UBAP2 and UBAP2L are the human orthologues of yeast Def1, and so identify the key missing proteins in the human last resort pathway.

Recovering local structure information from high-pressure total scattering experiments.

High pressure is a powerful thermodynamic tool for exploring the structure and the phase behaviour of the crystalline state, and is now widely used in conventional crystallographic measurements. High-pressure local structure measurements using neutron diffraction have, thus far, been limited by the presence of a strongly scattering, perdeuterated, pressure-transmitting medium (PTM), the signal from which contaminates the resulting pair distribution functions (PDFs). Here, a method is reported for subtracting the pairwise correlations of the commonly used 4:1 methanol:ethanol PTM from neutron PDFs obtained under hydro-static compression. The method applies a molecular-dynamics-informed empirical correction and a non-negative matrix factorization algorithm to recover the PDF of the pure sample. Proof of principle is demonstrated, producing corrected high-pressure PDFs of simple crystalline materials, Ni and MgO, and benchmarking these against simulated data from the average structure. Finally, the first local structure determination of α-quartz under hydro-static pressure is presented, extracting compression behaviour of the real-space structure.

Symmetry-adapted pair distribution function analysis (SAPA): a novel approach to evaluating lattice dynamics and local distortions from total scattering data.

A novel symmetry-adapted pair distribution function analysis (SAPA) method for extracting information on local distortions from pair distribution function data is introduced. The implementation of SAPA is demonstrated in the TOPAS-Academic software using the freely available online software ISODISTORT, and scripts for converting the output from ISODISTORT to a SAPA input file for TOPAS are provided. Finally, two examples are provided to show how SAPA can evaluate the nature of both dynamic distortions in ScF3 and the distortions which act as an order parameter for the phase transitions in BaTiO3.

Exploring cation disorder in mixed-metal pyrochlore ceramics using 17 O NMR spectroscopy and first-principles calculations.

Characterising the local structures (e.g., the cation distribution) of mixed-metal ceramics by NMR spectroscopy is often challenging owing to the unfavourable properties (low γ, large quadrupole moment and/or low abundance) of many metal nuclei. 17 O is an attractive option owing to the prevalence of oxygen within ceramics. The moderate γ and small quadrupole moment of 17 O mean that the greatest barrier to accessing the information available from this nucleus is isotopic enrichment. We explore the challenges of ensuring uniform isotopic enrichment with 17 O2 (g) for the pyrochlore solid solutions, Y2 Snx Ti2-x O7 , La2 Snx Zr2-x O7 and La2 Snx Hf2-x O7 , demonstrating that high enrichment temperatures (900 °C for 12 hr) are required. In addition, for sites with very high symmetry (such as the tetrahedral OY4 and OLa4 sites with CQ ≈ 0 present here), we demonstrate that quantitative 17 O NMR spectra require correction for the differing contributions from the centreband of the satellite transitions, which can be as high as a factor of ~3.89. It is common to use first-principles calculations to aid in interpreting NMR spectra of disordered solids. Here, we use an ensemble modelling approach to ensure that all possible cation arrangements are modelled in the minimum possible number of calculations. By combining uniform isotopic enrichment, quantitative NMR spectroscopy and a comprehensive computational approach, we are able to show that the cation distribution in Y2 Snx Ti2-x O7 is essentially random, whereas in La2 Snx Zr2-x O7 and La2 Snx Hf2-x O7 , OLa2SnZr and OLa2SnHf sites are slightly energetically disfavoured, leading to a weak preference for clustering of like cations.

Regulation of the RNAPII Pool Is Integral to the DNA Damage Response.

In response to transcription-blocking DNA damage, cells orchestrate a multi-pronged reaction, involving transcription-coupled DNA repair, degradation of RNA polymerase II (RNAPII), and genome-wide transcription shutdown. Here, we provide insight into how these responses are connected by the finding that ubiquitylation of RNAPII itself, at a single lysine (RPB1 K1268), is the focal point for DNA-damage-response coordination. K1268 ubiquitylation affects DNA repair and signals RNAPII degradation, essential for surviving genotoxic insult. RNAPII degradation results in a shutdown of transcriptional initiation, in the absence of which cells display dramatic transcriptome alterations. Additionally, regulation of RNAPII stability is central to transcription recovery-persistent RNAPII depletion underlies the failure of this process in Cockayne syndrome B cells. These data expose regulation of global RNAPII levels as integral to the cellular DNA-damage response and open the intriguing possibility that RNAPII pool size generally affects cell-specific transcription programs in genome instability disorders and even normal cells.

The Role of the Transcriptional Response to DNA Replication Stress.

During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.

Sustained E2F-Dependent Transcription Is a Key Mechanism to Prevent Replication-Stress-Induced DNA Damage.

Recent work established DNA replication stress as a crucial driver of genomic instability and a key event at the onset of cancer. Post-translational modifications play an important role in the cellular response to replication stress by regulating the activity of key components to prevent replication-stress-induced DNA damage. Here, we establish a far greater role for transcriptional control in determining the outcome of replication-stress-induced events than previously suspected. Sustained E2F-dependent transcription is both required and sufficient for many crucial checkpoint functions, including fork stalling, stabilization, and resolution. Importantly, we also find that, in the context of oncogene-induced replication stress, where increased E2F activity is thought to cause replication stress, E2F activity is required to limit levels of DNA damage. These data suggest a model in which cells experiencing oncogene-induced replication stress through deregulation of E2F-dependent transcription become addicted to E2F activity to cope with high levels of replication stress.

IP3 signalling regulates exogenous RNAi in Caenorhabditis elegans.

RNA interference (RNAi) is a widespread and widely exploited phenomenon. Here, we show that changing inositol 1,4,5-trisphosphate (IP3) signalling alters RNAi sensitivity in Caenorhabditis elegans. Reducing IP3 signalling enhances sensitivity to RNAi in a broad range of genes and tissues. Conversely up-regulating IP3 signalling decreases sensitivity. Tissue-specific rescue experiments suggest IP3 functions in the intestine. We also exploit IP3 signalling mutants to further enhance the sensitivity of RNAi hypersensitive strains. These results demonstrate that conserved cell signalling pathways can modify RNAi responses, implying that RNAi responses may be influenced by an animal's physiology or environment.