Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs we focused on the reprogramming factors ...OCT4 and SOX2. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling cryo-EM structure determination at two preferred positions. Depending on motif location, OCT4-SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from Histone H2A/Histone H3 (H2A/H3); however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA binding domains to engage DNA in both structures, reading-out a partial motif. These findings explain site specific nucleosome engagement by the pluripotency factors OCT4-SOX2 and reveal how TFs distort nucleosomes to access chromatinized motifs.
A major cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) spectrum disorder is the hexanucleotide G
4
C
2
repeat expansion in the first intron of the C9orf72 ...gene. Many underlying mechanisms lead to manifestation of disease that include toxic gain-of-function by repeat G
4
C
2
RNAs, dipeptide repeat proteins, and a reduction of the C9orf72 gene product. The C9orf72 protein interacts with SMCR8 and WDR41 to form a trimeric complex and regulates multiple cellular pathways including autophagy. Here, we report the structure of the C9orf72-SMCR8 complex at 3.8 Å resolution using single-particle cryo-electron microscopy (cryo-EM). The structure reveals 2 distinct dimerization interfaces between C9orf72 and SMCR8 that involves an extensive network of interactions. Homology between C9orf72-SMCR8 and Folliculin-Folliculin Interacting Protein 2 (FLCN-FNIP2), a GTPase activating protein (GAP) complex, enabled identification of a key residue within the active site of SMCR8. Further structural analysis suggested that a coiled-coil region within the uDenn domain of SMCR8 could act as an interaction platform for other coiled-coil proteins, and its deletion reduced the interaction of the C9orf72-SMCR8 complex with FIP200 upon starvation. In summary, this study contributes toward our understanding of the biological function of the C9orf72-SMCR8 complex.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Direct epitaxial growth of III-Vs on silicon for optical emitters and detectors is an elusive goal. Nanowires enable the local integration of high-quality III-V material, but advanced ...devices are hampered by their high-aspect ratio vertical geometry. Here, we demonstrate the in-plane monolithic integration of an InGaAs nanostructure
p-i-n
photodetector on Si. Using free space coupling, photodetectors demonstrate a spectral response from 1200-1700 nm. The 60 nm thin devices, with footprints as low as ~0.06 μm
2
, provide an ultra-low capacitance which is key for high-speed operation. We demonstrate high-speed optical data reception with a nanostructure photodetector at 32 Gb s
−1
, enabled by a 3 dB bandwidth exceeding ~25 GHz. When operated as light emitting diode, the
p-i-n
devices emit around 1600 nm, paving the way for future fully integrated optical links.
Ribosomes undergo multiple conformational transitions during translation elongation. Here, we report the high-resolution cryoelectron microscopy (cryo-EM) structure of the human 80S ribosome in the ...post-decoding pre-translocation state (classical-PRE) at 3.3-Å resolution along with the rotated (hybrid-PRE) and the post-translocation states (POST). The classical-PRE state ribosome structure reveals a previously unobserved interaction between the C-terminal region of the conserved ribosomal protein uS19 and the A- and P-site tRNAs and the mRNA in the decoding site. In addition to changes in the inter-subunit bridges, analysis of different ribosomal conformations reveals the dynamic nature of this domain and suggests a role in tRNA accommodation and translocation during elongation. Furthermore, we show that disease-associated mutations in uS19 result in increased frameshifting. Together, this structure-function analysis provides mechanistic insights into the role of the uS19 C-terminal tail in the context of mammalian ribosomes.
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•uS19 C-terminal tail undergoes dynamic rearrangement during translation elongation•uS19 C-terminal tail stabilizes the P-site tRNA and decoding interactions•Disease-associated mutations in uS19 C-terminal tail cause translational defects
In this study, Bhaskar et al. visualize the dynamic rearrangement of the uS19 C-terminal tail during translation elongation and elucidate its role in stabilizing aminoacyl tRNA and decoding interactions and in coordination of peptidyl tRNA movements within the mammalian ribosome during protein synthesis.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced ...pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA. Here we report cryo-electron microscopy structures of UV-DDB bound to nucleosomes bearing a 6-4 pyrimidine-pyrimidone dimer or a DNA-damage mimic in various positions. We find that UV-DDB binds UV-damaged nucleosomes at lesions located in the solvent-facing minor groove without affecting the overall nucleosome architecture. In the case of buried lesions that face the histone core, UV-DDB changes the predominant translational register of the nucleosome and selectively binds the lesion in an accessible, exposed position. Our findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes, and identify slide-assisted site exposure as a mechanism by which high-affinity DNA-binding proteins can access otherwise occluded sites in nucleosomal DNA.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The Vietnamese Mekong Delta (VMD) has been affected by environmental challenges for several decades, including coastal erosion and land subsidence. Subsidence rates of several cm/yr have been ...reported in parts of the delta, which are one order larger than the regional sea level rise of 3.3 mm/yr. The precise monitoring of subsidence with high spatial and temporal resolution is essential to understand its causes and associated risks, and to support the development and monitoring of countermeasures. Here, we present subsidence estimates between 2017 and 2022 derived from advanced persistent scatterer interferometry (PSI) applied to Sentinel-1 data. The PSI approach fully integrates temporary persistent scatterers, in order to derive the best possible persistent scatterer network for long time series. Furthermore, we adapted a method to optimally integrate reference points with known displacement to suppress spatially correlated nuisance (SCN) in the derived displacement time series. Due to a lack of geodetic references, we built an infrastructural reference network based on large bridges with piled foundations of about 70 m depth, which are only affected by compaction in deeper soil layers. We compare the method with the standard referencing approach in PSI, and show that referencing to the selected reference bridges with our method enables to measure the largest part of the subsidence while reducing the SCN considerably. We find the highest subsidence rates of more than 7 cm/yr mainly in urban areas, and various kinds of temporal nonlinearities.
Tunneling field-effect transistors (TunnelFET), a leading steep-slope transistor candidate, is still plagued by defect response, and there is a large discrepancy between measured and simulated device ...performance. In this work, highly scaled InAs/In x Ga1–x As y Sb1‑y/GaSb vertical nanowire TunnelFET with ability to operate well below 60 mV/decade at technically relevant currents are fabricated and characterized. The structure, composition, and strain is characterized using transmission electron microscopy with emphasis on the heterojunction. Using Technology Computer Aided Design (TCAD) simulations and Random Telegraph Signal (RTS) noise measurements, effects of different type of defects are studied. The study reveals that the bulk defects have the largest impact on the performance of these devices, although for these highly scaled devices interaction with even few oxide defects can have large impact on the performance. Understanding the contribution by individual defects, as outlined in this letter, is essential to verify the fundamental physics of device operation, and thus imperative for taking the III–V TunnelFETs to the next level.
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IJS, KILJ, NUK, PNG, UL, UM
Efficient, reproducible and accountable single-particle cryo-electron microscopy structure determination is tedious and often impeded by the lack of a standardized procedure for data analysis and ...processing. To address this issue, we have developed the FMI Live Analysis and Reconstruction Engine (CryoFLARE). CryoFLARE is a modular open-source platform offering easy integration of new processing algorithms developed by the cryo-EM community. It provides a user-friendly interface that allows fast setup of standardized workflows, serving the need of pharmaceutical industry and academia alike who need to optimize throughput of their microscope. To consistently document how data is processed, CryoFLARE contains an integrated reporting facility to create reports. Live analysis and processing parallel to data acquisition are used to monitor and optimize data quality. Problems at the level of the sample preparation (heterogeneity, ice thickness, sparse particles, areas selected for acquisition, etc.) or misalignments of the microscope optics can quickly be detected and rectified before data collection is continued. Interfacing with automated data collection software for retrieval of acquisition metadata reduces user input needed for analysis, and with it minimizes potential sources of errors and workflow inconsistencies. Local and remote export support in Relion-compatible job and data format allows seamless integration into the refinement process. The support for nonlinear workflows and fine-grained scheduling for mixed workflows with separate CPU and GPU based calculation steps ensures optimal use of processing hardware. CryoFLARE’s flexibility allows it to be used for all types of image acquisitions, ranging from sample screening to high-resolution data collection, and it offers a new alternative for setting up image processing workflows. It can be used without modifications of the hardware/software delivered by the microscope supplier. As it runs on a server in parallel to the hardware used for acquisition, it can easily be set up for remote display connections and fast control of the acquisition status.
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IJS, KILJ, NUK, PNG, UL, UM
In this paper a simulation study of the effect of conduction and valence band offsets on the subthreshold swing (SS) of a double-gate tunnel field-effect transistor (TFET) with gate-overlapped source ...is presented. The simulations show that if the pn-junction and the hetero-junction coincide, the band offsets can significantly improve the SS by suppressing the so-called point tunneling at the pn-junction. It turns out that the performance of an n-channel TFET is determined by the direct conduction band offset whereas that of a p-channel TFET is mainly effected by the energy difference between the light hole bands of the two materials. Thus, the performance of the hetero-junction TFET can be improved by selecting material systems with high conduction or valence band offsets. The misalignment between the pn-junction and the hetero-junction is shown to degrade the SS. The above-described band-offset engineering has been applied to the GeSn/SiGeSn hetero-structure system with and without strain. Simulations of GeSn/SiGeSn hetero-TFETs with band-to-band-tunneling parameters determined from pseudopotential calculations show that compressive strain in GeSn widens the design space for TFET application while tensile strain reduces it.
Ribosomes are the macromolecular machines at the heart of protein synthesis; however, their function can be modulated by a variety of additional protein factors that directly interact with them. ...Here, we report the cryo-EM structure of human Ebp1 (p48 isoform) bound to the human 80S ribosome at 3.3 Å resolution. Ebp1 binds in the vicinity of the peptide exit tunnel on the 80S ribosome, and this binding is enhanced upon puromycin-mediated translational inhibition. The association of Ebp1 with the 80S ribosome centers around its interaction with ribosomal proteins eL19 and uL23 and the 28S rRNA. Further analysis of the Ebp1-ribosome complex suggests that Ebp1 can rotate around its insert domain, which may enable it to assume a wide range of conformations while maintaining its interaction with the ribosome. Structurally, Ebp1 shares homology with the methionine aminopeptidase 2 family of enzymes; therefore, this inherent flexibility may also be conserved.
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