Readout of epigenetic modifications.

This review focuses on a structure-based analysis of histone posttranslational modification (PTM) readout, where the PTMs serve as docking sites for reader modules as part of larger complexes displaying chromatin modifier and remodeling activities, with the capacity to alter chromatin architecture and templated processes. Individual topics addressed include the diversity of reader-binding pocket architectures and common principles underlying readout of methyl-lysine and methyl-arginine marks, their unmodified counterparts, as well as acetyl-lysine and phosphoserine marks. The review also discusses the impact of multivalent readout of combinations of PTMs localized at specific genomic sites by linked binding modules on processes ranging from gene transcription to repair. Additional topics include cross talk between histone PTMs, histone mimics, epigenetic-based diseases, and drug-based therapeutic intervention. The review ends by highlighting new initiatives and advances, as well as future challenges, toward the promise of enhancing our structural and mechanistic understanding of the readout of histone PTMs at the nucleosomal level.

Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.

Histone methyltransferases of the nuclear receptor-binding SET domain protein (NSD) family, including NSD1, NSD2 and NSD3, have crucial roles in chromatin regulation and are implicated in oncogenesis1,2. NSD enzymes exhibit an autoinhibitory state that is relieved by binding to nucleosomes, enabling dimethylation of histone H3 at Lys36 (H3K36)3-7. However, the molecular basis that underlies this mechanism is largely unknown. Here we solve the cryo-electron microscopy structures of NSD2 and NSD3 bound to mononucleosomes. We find that binding of NSD2 and NSD3 to mononucleosomes causes DNA near the linker region to unwrap, which facilitates insertion of the catalytic core between the histone octamer and the unwrapped segment of DNA. A network of DNA- and histone-specific contacts between NSD2 or NSD3 and the nucleosome precisely defines the position of the enzyme on the nucleosome, explaining the specificity of methylation to H3K36. Intermolecular contacts between NSD proteins and nucleosomes are altered by several recurrent cancer-associated mutations in NSD2 and NSD3. NSDs that contain these mutations are catalytically hyperactive in vitro and in cells, and their ectopic expression promotes the proliferation of cancer cells and the growth of xenograft tumours. Together, our research provides molecular insights into the nucleosome-based recognition and histone-modification mechanisms of NSD2 and NSD3, which could lead to strategies for therapeutic targeting of proteins of the NSD family.

A poised chromatin platform for TGF-ß access to master regulators.

Specific chromatin marks keep master regulators of differentiation silent yet poised for activation by extracellular signals. We report that nodal TGF-ß signals use the poised histone mark H3K9me3 to trigger differentiation of mammalian embryonic stem cells. Nodal receptors induce the formation of companion Smad4-Smad2/3 and TRIM33-Smad2/3 complexes. The PHD-Bromo cassette of TRIM33 facilitates binding of TRIM33-Smad2/3 to H3K9me3 and H3K18ac on the promoters of mesendoderm regulators Gsc and Mixl1. The crystal structure of this cassette, bound to histone H3 peptides, illustrates that PHD recognizes K9me3, and Bromo binds an adjacent K18ac. The interaction between TRIM33-Smad2/3 and H3K9me3 displaces the chromatin-compacting factor HP1γ, making nodal response elements accessible to Smad4-Smad2/3 for Pol II recruitment. In turn, Smad4 increases K18 acetylation to augment TRIM33-Smad2/3 binding. Thus, nodal effectors use the H3K9me3 mark as a platform to switch master regulators of stem cell differentiation from the poised to the active state.

Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression.

The MLL1 gene is a frequent target for recurrent chromosomal translocations, resulting in transformation of hematopoietic precursors into leukemia stem cells. Here, we report on structure-function studies that elucidate molecular events in MLL1 binding of histone H3K4me3/2 marks and recruitment of the cyclophilin CyP33. CyP33 contains a PPIase and a RRM domain and regulates MLL1 function through HDAC recruitment. We find that the PPIase domain of CyP33 regulates the conformation of MLL1 through proline isomerization within the PHD3-Bromo linker, thereby disrupting the PHD3-Bromo interface and facilitating binding of the MLL1-PHD3 domain to the CyP33-RRM domain. H3K4me3/2 and CyP33-RRM target different surfaces of MLL1-PHD3 and can bind simultaneously to form a ternary complex. Furthermore, the MLL1-CyP33 interaction is required for repression of HOXA9 and HOXC8 genes in vivo. Our results highlight the role of PHD3-Bromo cassette as a regulatory platform, orchestrating MLL1 binding of H3K4me3/2 marks and cyclophilin-mediated repression through HDAC recruitment.

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain.

The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.

Sub-60-fs mode-locked Tm,Ho:CaYLuAlO4 laser at 2.05†µm.

Tm,Ho:CaYLuAlO4 (Tm,Ho:CALYLO) crystal has wide emission spectra both for π-polarization and σ-polarization, showing significant potential for the generation of ultrashort pulses. Here, a widely tunable and passively mode-locked laser operation based on Tm,Ho:CALYLO crystal under two polarizations was demonstrated for what we believe to be the first time ever. For π-polarization, a maximum output power of 1.52 W and a tuning range of 255.3 nm were achieved in the continuous wave (CW) regime. In the mode-locked regime, a pulse duration of 68 fs and an average output power of 228 mW were achieved upon GaSb-based semiconductor saturable absorber mirror (SESAM). As for σ-polarization, a broader tuning range of 267.1 nm was realized, leading to the shorter pulse duration of 58 fs at 79.7 MHz repetition rate.

Wavelength-tunable Tm:Y2O3 ceramic vortex laser with a changeable orbital angular momentum state.

Wavelength-tunable orbital angular momentum (OAM) lasers with controllable topological charges have the potential for serving as light sources for large-capacity optical communication by combining conventional wavelength division multiplexing (WDM) with OAM mode-division multiplexing (OAM-MDM). In this study, we demonstrate a wavelength-tunable Tm-bulk laser that can control OAM states in the 2-µm spectral range. The excitation conditions for different Laguerre-Gaussian (L G 0,l ) modes in a bulk laser cavity are theoretically determined by measuring the spatial propagation dynamics of the annular pump beam. As a proof-of-principle study, we experimentally generate OAM states of |ℏ| and |2ℏ| from a T m:Y 2 O 3 ceramic laser with a tunable emission wavelength using a Lyot filter (LF). The spatial properties of the scalar optical vortices are well conserved during wavelength tuning, indicating the feasibility of our approach for producing wavelength-tunable structured light. These OAM laser sources, which are characterized by their robustness and compactness, have potential applications in various areas such as optical communications, quantum optics, super-resolution microscopes, and more.

Structural basis of the human negative elongation factor NELF-B/C/E ternary complex.

Negative elongation factor (NELF) is a four-subunit transcription elongation factor that mainly functions in maintaining the paused state of RNA polymerase II in eukaryotes. Upon binding to Pol II, NELF works synergistically with DRB sensitivity-inducing factor (DSIF) and inhibits transcription elongation of Pol II, which subsequently retains a stably paused state 20-60 base pairs downstream of the promoter. The promoter-proximal pausing of Pol II caused by NELF is a general mechanism of transcriptional regulation for most signal-responsive genes. To date, structural studies have significantly advanced our understanding of the molecular mechanisms of NELF. However, a high quality structural model clarifying the interaction details of this complex is still lacking. In this study, we solved the high resolution crystal structure of the NELF-B/C/E ternary complex. We observed detailed interactions between subunits and identified residues important for the association between NELF-B and NELF-E. Our work presents a precise model of the NELF complex, which will facilitate our understanding of its in vivo function.

Reduction of depolarization loss in a Tm-doped sesquioxide ceramic laser using a ring-shaped pump beam.

We report on a simple method for reduction of the depolarization loss in an end-pumped Tm:Y2O3 ceramic laser by using a near-field ring-shaped pump beam. Initially, we theoretically derive the expression of the depolarization loss in a bulk laser end-pumped with a near-field flat-top-hat or ring-shaped beam, where a significant reduction of depolarization loss in the latter case is presented. Experimental verification is thereafter carried out with a Tm:Y2O3 ceramic laser employing these two different pump configurations. It shows that the experimentally measured depolarization losses are close to the simulated values; the loss in the case of the annular-beam pump is almost 18 times lower than that with a quasi-top-hat beam at a same absorption pump power of 7.4 W. This work, as a proof-of-principle study, indicates that depolarization loss in the end-pumped bulk lasers can be significantly reduced simply by using a ring-shaped pump beam.

Mode-locking of a Tm,Ho:CALYGO laser delivering 50 fs pulses at 2.08 µm.

We study the polarization-dependent laser performance of a novel, to the best of our knowledge, "mixed" Tm,Ho:CaYGdAlO4 crystal in the continuous-wave (CW) and mode-locked regimes. Both in terms of the CW tunability range (261 nm) and the minimum pulse duration (50 fs at 2078 nm, spectral width of 95 nm) in the mode-locked regime, σ-polarization is superior. With extended inhomogeneous spectral broadening due to structural and compositional disorder, Tm,Ho:CaYGdAlO4 is promising for few-optical-cycle pulse generation around 2 µm.

Genomic analysis and characterization of bacteriophage vB_SpuS_NX263 infecting Salmonella enterica subsp. enterica serovar Pullorum.

In this study, a new Salmonella phage, NX263, was isolated from sewage. This phage could lyse 90.57% (48/53) of the bacterial strains tested and showed good activity over a wide range of temperature (up to 60°C) and pH (5-10). Phylogenetic analysis showed that it should be classified as a member of the genus Skatevirus. The genome of phage NX263 is 46,574 bp in length with a GC content of 45.52%. It contains 89 open reading frames and two tRNA genes. No lysogeny, drug resistance, or virulence-associated genes were identified in the genome sequence, suggesting that this phage could potentially be used to treat Salmonella Pullorum infections.

The attenuated live vaccine strain W2512 provides protection against novel variant infectious bursal disease virus.

Infectious bursal disease virus (IBDV) causes an acute and highly contagious infectious disease characterized by severe immunosuppression, causing great economic losses to the poultry industry globally. Over the past 30 years, this disease has been well controlled through vaccination and strict biosafety measures. However, novel variant IBDV strains have emerged in recent years, posing a new threat to the poultry industry. Our previous epidemiological survey showed that few novel variant IBDV strains had been isolated from chickens immunized with the attenuated live vaccine W2512-, suggesting that this vaccine is efficacious against novel variant strains. Here, we report the protective effect of the W2512 vaccine against novel variant strains in SPF chickens and commercial yellow-feathered broilers. We found that W2512 causes severe atrophy of the bursa of Fabricius in SPF chickens and commercial yellow-feathered broilers, induces high levels of antibodies against IBDV, and protects chickens from infection with the novel variant strains via a placeholder effect. This study highlights the protective effect of commercial attenuated live vaccines against the novel IBDV variant and provides guidance for the prevention and control of this disease.

Polycomb-like proteins link the PRC2 complex to CpG islands.

The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as PHF1, MTF2 and PHF19, are PRC2-associated factors that form sub-complexes with PRC2 core components, and have been proposed to modulate the enzymatic activity of PRC2 or the recruitment of PRC2 to specific genomic loci. Mammalian PRC2-binding sites are enriched in CG content, which correlates with CpG islands that display a low level of DNA methylation. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. Here we solve the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We show that the extended homologous regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a completely different manner from the canonical winged-helix DNA recognition motif. We also show that the PCL extended homologous domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic stem cells. Our research provides the first, to our knowledge, direct evidence to demonstrate that PCL proteins are crucial for PRC2 recruitment to CpG islands, and further clarifies the roles of these proteins in transcriptional regulation in vivo.

Structural Basis of the Transcriptional Elongation Factor Paf1 Core Complex from Saccharomyces eubayanus.

The multicomponent polymerase associated factor 1 (Paf1) complex (PAF1C) is an important transcription elongation factor that upregulates RNA polymerase II-mediated genome-wide transcription. PAF1C can regulate transcription through direct association with the polymerase or by impacting the chromatin structure epigenetically. In recent years, significant progress has been made in understanding the molecular mechanisms of PAF1C. However, high-resolution structures that can clarify the interaction details among the components of the complex are still needed. In this study, we evaluated the structural core of the yeast PAF1C containing the four components Ctr9, Paf1, Cdc73 and Rtf1 at high resolution. We observed the interaction details among these components. In particular, we identified a new binding surface of Rtf1 on PAF1C and found that the C-terminal sequence of Rtf1 dramatically changed during evolution, which may account for its different binding affinities to PAF1C among species. Our work presents a precise model of PAF1C, which will facilitate our understanding of the molecular mechanism and the in vivo function of the yeast PAF1C.

63 W wing-pumped Tm:YAG single-crystal fiber laser.

We present a high-power continuous-wave (CW) Tm:YAG single-crystal fiber (SCF) laser wing-pumped by laser diodes at 791 nm. A maximum output power of 63.3 W is achieved at ∼ 2.01 µm, corresponding to a slope efficiency of 34.2%. This is, to the best of our knowledge, the highest power obtained from the SCF laser in the 2 µm spectral range. In addition to the wing pumping scheme, the large surface-to-volume ratio of such fiber-geometry crystalline rod with diffusion-bonded undoped YAG end caps are benefited for the spatial uniform distribution of pump intensity and thermal load, and thus improving the power scalability.

Ho:LuAG single crystal fiber: growth, spectroscopy and laser characteristics.

Lutetium aluminum garnet single-crystal fiber (SCF, ∼ Φ 0.9 mm - 165 mm) doped with 0.5 at.% Ho3+ has been grown by the micro-pulling-down (µ-PD) technique. The room-temperature absorption and emission spectra exhibit similar features to the bulk crystal. Laser performances of the SCFs with two different pump configurations, i.e., pump guiding and free-space propagation, are studied by employing a 1.9-µm laser diode and a high-brightness fiber laser, respectively. Laser slope efficiencies obtained with both pump configurations can be higher than 50%, and a maximum output power of 6.01 W is achieved at ∼ 2.09 µm with the former pump. The comparable efficiency to the high-brightness pump is an indication of that high laser performance can also be expected through pump-guiding in the SCF even with a low pump beam quality.

Watt-level femtosecond Tm-doped "mixed" sesquioxide ceramic laser in-band pumped by a Raman fiber laser at 1627 nm.

We report on a semiconductor saturable absorber mirror mode-locked Tm:(Lu,Sc)2O3 ceramic laser in-band pumped by a Raman fiber laser at 1627 nm. The nonlinear refractive index (n2) of the Tm:(Lu,Sc)2O3 ceramic has been measured to be 4.66 × 10-20 m2/W at 2000 nm. An average output power up to 1.02 W at 2060 nm is achieved for transform-limited 280-fs pulses at a repetition rate of 86.5 MHz, giving an optical efficiency with respect to the absorbed pump power of 36.4%. Pulses as short as 66 fs at 2076 nm are produced at the expense of output power (0.3 W), corresponding to a spectral bandwidth of 69 nm. The present work reveals the potential of Tm3+-doped sesquioxide transparent ceramics for power scaling of femtosecond mode-locked bulk lasers emitting in the 2-µm spectral range.

SESAM mode-locked Tm:Y2O3 ceramic laser.

We demonstrate a widely tunable and passively mode-locked Tm:Y2O3 ceramic laser in-band pumped by a 1627-nm Raman fiber laser. A tuning range of 318 nm, from 1833 to 2151 nm, is obtained in the continuous-wave regime. The SESAM mode-locked laser produces Fourier-transform-limited pulses as short as 75 fs at ∼ 2.06 µm with an average output power of 0.26 W at 86.3 MHz. For longer pulse durations of 178 fs, an average power of 0.59 W is achieved with a laser efficiency of 29%. This is, to the best of our knowledge, the first mode-locked Tm:Y2O3 laser in the femtosecond regime. The spectroscopic properties and laser performance confirm that Tm:Y2O3 transparent ceramics are a promising gain material for ultrafast lasers at 2 µm.

Cryo-EM Structure of Actin Filaments from Zea mays Pollen.

Actins are among the most abundant and conserved proteins in eukaryotic cells, where they form filamentous structures that perform vital roles in key cellular processes. Although large amounts of data on the biochemical activities, dynamic behaviors, and important cellular functions of plant actin filaments have accumulated, their structural basis remains elusive. Here, we report a 3.9 Å structure of the plant actin filament from Zea mays pollen (ZMPA) using cryo-electron microscopy. The structure shows a right-handed, double-stranded (two parallel strands) and staggered architecture that is stabilized by intra- and interstrand interactions. While the overall structure resembles that of other actin filaments, its DNase I binding loop bends farther outward, adopting an open conformation similar to that of the jasplakinolide- or beryllium fluoride (BeFx)-stabilized rabbit skeletal muscle actin (RSMA) filament. Single-molecule magnetic tweezers analysis revealed that the ZMPA filament can resist a greater stretching force than the RSMA filament. Overall, these data provide evidence that plant actin filaments have greater stability than animal actin filaments, which might be important to their role as tracks for long-distance vesicle and organelle transportation.plantcell;31/12/2855/FX1F1fx1.

Fe-N complex biochar as a superior partner of sodium sulfide for methyl orange decolorization by combination of adsorption and reduction.

To enhance the decolorization of methyl orange (MO), Fe-N complex biochar (Fe-N-BC) was developed as an accelerator in the sodium sulfide (Na2S) reduction system. The decolorization effect and mechanism of MO in the Fe-N-BC/Na2S composite system were studied. Surface pore analysis, Raman spectroscopy, FT-IR, XPS, and electrochemical analysis were used to characterize Fe-N-BC and unmodified biochar (BC). These results demonstrated that Fe-N-BC had better adsorption performance (specific surface area 463.46 m2 g-1) and electron transfer capacity than BC. By adding Fe-N-BC to the Na2S reduction system for MO, it was found that the decolorization of MO was greatly improved (increased by 93%). Besides, the effects of critical factors such as the initial concentration of Na2S, the dosage of Fe-N-BC, pH value, and temperature on the decolorization rate of MO were evaluated. Through the analysis of the action mechanism, the cooperation mode of Fe-N-BC and Na2S was to form an infinite cycle of adsorption-reduction-regeneration, so as to realize the rapid decolorization of MO. On the one hand, Fe-N-BC could adsorb MO and Na2S on its surface to increase the contact opportunity; on the other hand, it could act as a redox mediator to accelerate the electron transfer of the reduction reaction. In addition, the degradation of MO by Na2S was also an in-situ regeneration of Fe-N-BC. These findings may provide a feasible method to decolorize azo dyes quickly by cooperating with chemical reducing agents from a new perspective.