Initiation of Parental Genome Reprogramming in Fertilized Oocyte by Splicing Kinase SRPK1-Catalyzed Protamine Phosphorylation.

The paternal genome undergoes a massive exchange of histone with protamine for compaction into sperm during spermiogenesis. Upon fertilization, this process is potently reversed, which is essential for parental genome reprogramming and subsequent activation; however, it remains poorly understood how this fundamental process is initiated and regulated. Here, we report that the previously characterized splicing kinase SRPK1 initiates this life-beginning event by catalyzing site-specific phosphorylation of protamine, thereby triggering protamine-to-histone exchange in the fertilized oocyte. Interestingly, protamine undergoes a DNA-dependent phase transition to gel-like condensates and SRPK1-mediated phosphorylation likely helps open up such structures to enhance protamine dismissal by nucleoplasmin (NPM2) and enable the recruitment of HIRA for H3.3 deposition. Remarkably, genome-wide assay for transposase-accessible chromatin sequencing (ATAC-seq) analysis reveals that selective chromatin accessibility in both sperm and MII oocytes is largely erased in early pronuclei in a protamine phosphorylation-dependent manner, suggesting that SRPK1-catalyzed phosphorylation initiates a highly synchronized reorganization program in both parental genomes.

Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109.

Rtt109 is a unique histone acetyltransferase acetylating histone H3 lysine 56 (H3K56), a modification critical for DNA replication-coupled nucleosome assembly and genome stability. In cells, histone chaperone Asf1 is essential for H3K56 acetylation, yet the mechanisms for H3K56 specificity and Asf1 requirement remain unknown. We have determined the crystal structure of the Rtt109-Asf1-H3-H4 complex and found that unwinding of histone H3 αN, where K56 is normally located, and stabilization of the very C-terminal ß strand of histone H4 by Asf1 are prerequisites for H3K56 acetylation. Unexpectedly, an interaction between Rtt109 and the central helix of histone H3 is also required. The observed multiprotein, multisite substrate recognition mechanism among histone modification enzymes provides mechanistic understandings of Rtt109 and Asf1 in H3K56 acetylation, as well as valuable insights into substrate recognition by histone modification enzymes in general.

Topography of histone H3-H4 interaction with the Hat1-Hat2 acetyltransferase complex.

Chaperones influence histone conformation and intermolecular interaction in multiprotein complexes, and the structures obtained with full-length histones often provide more accurate and comprehensive views. Here, our structure of the Hat1-Hat2 acetyltransferase complex bound to Asf1-H3-H4 shows that the core domains of H3 and H4 are involved in binding Hat1 and Hat2, and the N-terminal tail of H3 makes extensive interaction with Hat2. These findings expand the knowledge about histone-protein interaction and implicate a function of Hat2/RbAp46/48, which is a versatile histone chaperone found in many chromatin-associated complexes, in the passing of histones between chaperones.

Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase.

Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification1-3. The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome4, counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1)5 to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. 6-9). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3-H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A-H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1.

Distinct histone H3-H4 binding modes of sNASP reveal the basis for cooperation and competition of histone chaperones.

Chromosomal duplication requires de novo assembly of nucleosomes from newly synthesized histones, and the process involves a dynamic network of interactions between histones and histone chaperones. sNASP and ASF1 are two major histone H3-H4 chaperones found in distinct and common complexes, yet how sNASP binds H3-H4 in the presence and absence of ASF1 remains unclear. Here we show that, in the presence of ASF1, sNASP principally recognizes a partially unfolded Nα region of histone H3, and in the absence of ASF1, an additional sNASP binding site becomes available in the core domain of the H3-H4 complex. Our study also implicates a critical role of the C-terminal tail of H4 in the transfer of H3-H4 between sNASP and ASF1 and the coiled-coil domain of sNASP in nucleosome assembly. These findings provide mechanistic insights into coordinated histone binding and transfer by histone chaperones.

Structural Basis for pri-miRNA Recognition by Drosha.

A commencing and critical step in miRNA biogenesis involves processing of pri-miRNAs in the nucleus by Microprocessor. An important, but not completely understood, question is how Drosha, the catalytic subunit of Microprocessor, binds pri-miRNAs and correctly specifies cleavage sites. Here we report the cryoelectron microscopy structures of the Drosha-DGCR8 complex with and without a pri-miRNA. The RNA-bound structure provides direct visualization of the tertiary structure of pri-miRNA and shows that a helix hairpin in the extended PAZ domain and the mobile basic (MB) helix in the RNase IIIa domain of Drosha coordinate to recognize the single-stranded to double-stranded junction of RNA, whereas the dsRNA binding domain makes extensive contacts with the RNA stem. Furthermore, the RNA-free structure reveals an autoinhibitory conformation of the PAZ helix hairpin. These findings provide mechanistic insights into pri-miRNA cleavage site selection and conformational dynamics governing pri-miRNA recognition by the catalytic component of Microprocessor.

The postsynaptic density proteins Homer and Shank form a polymeric network structure.

The postsynaptic density (PSD) is crucial for synaptic functions, but the molecular architecture retaining its structure and components remains elusive. Homer and Shank are among the most abundant scaffolding proteins in the PSD, working synergistically for maturation of dendritic spines. Here, we demonstrate that Homer and Shank, together, form a mesh-like matrix structure. Crystallographic analysis of this region revealed a pair of parallel dimeric coiled coils intercalated in a tail-to-tail fashion to form a tetramer, giving rise to the unique configuration of a pair of N-terminal EVH1 domains at each end of the coiled coil. In neurons, the tetramerization is required for structural integrity of the dendritic spines and recruitment of proteins to synapses. We propose that the Homer-Shank complex serves as a structural framework and as an assembly platform for other PSD proteins.

Synchronous Driving Method for Stitching Pixel Arrays Based on an Adaptive Correction Technique.

With the application of stitching technology in large-pixel-array CMOS image sensors, the problem of non-synchronized output signals from pixel array bilateral driver circuits has become progressively more serious and has led to the DC perforation of bilateral driver circuits, while conventional clock tree synchronization design methodology does not apply to stitching technology. Therefore, this paper analyses reasons for the inconsistency in the output signals of bilateral driving circuits and proposes a synchronous driving method applicable to stitching pixel arrays based on the idea of on-chip output signal delay detection and calibration. This method detects and corrects the non-synchrony of the row driver output signals on both sides according to changes in the operating environment of the chip. This method is characterized by a simple structure and high reliability. Finally, based on the 55 nm stitching process, simulations are carried out in a CMOS image sensor with a chip area of 77 mm × 84 mm to verify that this method is feasible. This large image sensor with a 150 M pixel array has a frame rate of over 10 FPS.

Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5.

Assembly of the spliceosomal small nuclear ribonucleoparticle (snRNP) core requires the participation of the multisubunit SMN (survival of motor neuron) complex, which contains SMN and several Gemin proteins. The SMN and Gemin2 subunits directly bind Sm proteins, and Gemin5 is required for snRNP biogenesis and has been implicated in snRNA recognition. The RNA sequence required for snRNP assembly includes the Sm site and an adjacent 3' stem-loop, but a precise understanding of Gemin5's RNA-binding specificity is lacking. Here we show that the N-terminal half of Gemin5, which is composed of two juxtaposed seven-bladed WD40 repeat domains, recognizes the Sm site. The tandem WD40 repeat domains are rigidly held together to form a contiguous RNA-binding surface. RNA-contacting residues are located mostly on loops between ß strands on the apical surface of the WD40 domains. Structural and biochemical analyses show that base-stacking interactions involving four aromatic residues and hydrogen bonding by a pair of arginines are crucial for specific recognition of the Sm sequence. We also show that an adenine immediately 5' to the Sm site is required for efficient binding and that Gemin5 can bind short RNA oligos in an alternative mode. Our results provide mechanistic understandings of Gemin5's snRNA-binding specificity as well as valuable insights into the molecular mechanism of RNA binding by WD40 repeat proteins in general.

Endowing Nanoparticles with High Stability on the Hydrogenation Reaction by the Amino Group-Assisted Strategy.

In the field of a heterogeneous industrial catalysis process, the encapsulated structure plays a crucial role in preventing active sites from leaching during the reaction; however, related studies on the strategy to fabricate encapsulated catalysts under control remain rare. Herein, we develop an amino-assisted strategy to construct a highly stable catalyst with core-shell copper nanoparticles (NPs), namely, Cu@NC (NC represents the nitrogen-doped carbon), presenting not only excellent activity but also high durability on the hydrogenation of quinolines even in the large-scale tests, which is very vital in practical application. In contrast, in the absence of the amino group, the Cu NPs were dispersed out of the carbon surface to form Cu/NC, leading to readily lose activity in the recycling tests due to the leaching occurred during the catalytic process. This work offers a promising method to fabricate a stable catalyst to enhance durability in heterogeneous catalysis.

Intermetallic Compound with CuNi Sites for Enhancing the Selectivity of Electrochemical CO2 Conversion.

Although single-metal-site (SMS) catalysts have long been explored for the electrochemical CO2 reduction reaction (EC-CO2RR), the reactivity and selectivity of SMS catalysts remain rather low due to the competing hydrogen evolution reaction (HER). To improve the selectivity, in this work, a novel intermetallic particle of CuNi is decorated on the N-doped carbon substrate, which was first precisely fabricated by scarifying the bimetal-doped metal-organic framework (MOF). Thanks to the neighboring synergistic functions of Cu and Ni sites, CuNi/NC prominently boosts the electroreduction of CO2, far more than the SMS catalysts of Cu/NC and Ni/NC. Further, CuNi/NC presents superior selectivity toward CO with faradaic efficiency over a wide range of potentials (surpassing 90% at 0.6-1.0 V vs RHE, up to 98% at 0.6 V vs RHE) and excellent durability. The experimental results and theoretical calculations reveal that the Ni species can be highly activated due to the neighboring Cu species, which considerably facilitates the formation of an intermediate of COOH* and consequently enhances the selectivity of the reduction of CO2 to CO. This work paves a general way to precisely fabricate catalysts with multiple metal species and also demonstrates the significant synergetic efficiency between the neighboring sites to improve the catalytic performance.

Energy landscape quantifications of histone H3.3 recognition by chaperone DAXX reveal an uncoupled binding specificity and affinity.

Histone variant H3.3 differs from the canonical histone H3.1 by only five amino acids, yet its chaperone death domain-associated protein (DAXX) can specifically recognize H3.3 over H3.1, despite having a large DAXX-interacting surface on the H3.3-H4 heterodimer common to that on the H3.1-H4 complex. This observation gives rise to the question of, from the binding energy point view, how high binding specificity may be achieved with small differences of the overall binding energy for protein-protein interactions in general. Here we investigate the mechanism of coupling of binding specificity and affinity in protein-protein interactions using the DAXX-H3.3-H4 complex as a model. Using a multi-scale method, we found that the hydrophobic interactions between DAXX and the H3.3-specific region contributed to their initial binding process. And the structural flexibility of the interacting partners contributed to the binding affinity after their encounter. By quantifying the free energy landscape, we revealed that the interaction between the specific residues of H3.3 and DAXX decreased the encounter barrier height while the folding of H3.3-H4 and DAXX increased the depth of the free energy basin of the final binding state. The encounter barrier height, which is not coupled to the thermodynamic stability of the final binding state, had a marked effect on the initial binding rate of flexible histones and chaperones. Based on the energy landscape theory, we found that the intrinsic binding energy funnel of this uncoupled recognition process was affected by the structural flexibility and the flexibility modulated the degree of coupling between binding specificity and affinity. Our work offers a biophysical explanation of the specific recognition between the histones and their chaperones, and also extends the use of energy landscape theory for understanding molecular recognitions in general.

Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex.

The SLX1-SLX4 structure-specific endonuclease complex is involved in processing diverse DNA damage intermediates, including resolution of Holliday junctions, collapse of stalled replication forks and removal of DNA flaps. The nuclease subunit SLX1 is inactive on its own, but become activated upon binding to SLX4 via its conserved C-terminal domain (CCD). Yet, how the SLX1-SLX4 complex recognizes specific DNA structure and chooses cleavage sites remains unknown. Here we show, through a combination of structural, biochemical and computational analyses, that the SAP domain of SLX4 is critical for efficient and accurate processing of 5'-flap DNA. It binds the minor groove of DNA about one turn away from the flap junction, and the 5'-flap is implicated in binding the core domain of SLX1. This binding mode accounts for specific recognition of 5'-flap DNA and specification of cleavage site by the SLX1-SLX4 complex.

High-Speed Fully Differential Two-Step ADC Design Method for CMOS Image Sensor.

The application requirements of high frame rate CMOS image sensors (CIS) in the industry have not been satisfied due to the speed limitations in traditional single-slope and serial two-step analog-to-digital converters (ADCs). In this paper, a high-speed fully differential two-step ADC design method for CIS was proposed. The proposed method was based on differential ramp and time-to-digital conversion (TDC) technology. A parallel conversion mode was formed that is different from serial conversion, and the robustness of the system was ensured due to the existence of differential ramps. Aiming at the inconsistency between traditional TDC technology and single-slope ADC, a TDC technology based on level coding was proposed. The proposed technology achieves the TDC in the last clock cycle of analog-to-digital conversion, and realized a two-step conversion process at another level. This paper presents a complete circuit design, layout design, and test verification of the proposed design method based on the 55 nm 1P4M CMOS experimental platform. Under the design environment of the analog voltage of 3.3 V, the digital voltage of 1.2 V, the clock frequency of 100 MHz, and a dynamic input range of 1.6 V, this design was a 12-bit ADC with a conversion time of 480 ns, column-level power consumption of 62 µW, differential nonlinearity (DNL) of +0.6/-0.6 LSB, and integral nonlinearity (INL) of +1.2/-1.4 LSB. Furthermore, it achieved a signal-to-noise distortion ratio (SNDR) of 70.08 dB. The proposed design provided a large area array with a high frame rate, and compared with the existing advanced single-slope ADC, its conversion speed increased by more than 52%. It provides an effective solution for the implementation of high frame frequency CIS.

High Dynamic Pixel Structure Based on an Adaptive Integrating Capacitor.

Infrared image sensing technology has received widespread attention due to its advantages of not being affected by the environment, good target recognition, and high anti-interference ability. However, with the improvement of the integration of the infrared focal plane, the dynamic range of the photoelectric system is difficult to improve, that is, the restrictive trade-off between noise and full well capacity is particularly prominent. Since the capacitance of the inversion MOS capacitor changes with the gate-source voltage adaptively, the inversion MOS capacitor is used as the capacitor in the infrared pixel circuit, which can solve the contradiction between noise in low light and full well capacity in high light. To this end, a highly dynamic pixel structure based on adaptive capacitance is proposed, so that the capacitance of the infrared image sensor can automatically change from 6.5 fF to 37.5 fF as the light intensity increases. And based on 55 nm CMOS process technology, the performance parameters of an infrared image sensor with a 12,288 × 12,288 pixel array are studied. The research results show that a small-size pixel of 5.5 µm × 5.5 µm has a large full well capacity of 1.31 Me- and a variable conversion gain, with a noise of less than 0.43 e- and a dynamic range of more than 130 dB.

High-Linearity and High-Speed ROIC of Ultra-Large Array Infrared Detectors Based on Adaptive Compensation and Enhancement.

In order to solve the problem of limited linearity and frame rate in the large array infrared (IR) readout integrated circuit (ROIC), a high-linearity and high-speed readout method based on adaptive offset compensation and alternating current (AC) enhancement is proposed in this paper. The efficient correlated double sampling (CDS) method in pixels is used to optimize the noise characteristics of the ROIC and output CDS voltage to the column bus. An AC enhancement method is proposed to quickly establish the column bus signal, and an adaptive offset compensation method is used at the column bus terminal to eliminate the nonlinearity caused by the pixel source follower (SF). Based on the 55 nm process, the proposed method is comprehensively verified in an 8192 × 8192 IR ROIC. The results show that, compared with the traditional readout circuit, the output swing is increased from 2 V to 3.3 V, and the full well capacity is increased from 4.3 Me- to 6 Me-. The row time of the ROIC is reduced from 20 µs to 2 µs, and the linearity is improved from 96.9% to 99.98%. The overall power consumption of the chip is 1.6 W, and the single-column power consumption of the readout optimization circuit is 33 µW in the accelerated readout mode and 16.5 µW in the nonlinear correction mode.

Structural basis for allosteric, substrate-dependent stimulation of SIRT1 activity by resveratrol.

Sirtuins with an extended N-terminal domain (NTD), represented by yeast Sir2 and human SIRT1, harbor intrinsic mechanisms for regulation of their NAD-dependent deacetylase activities. Elucidation of the regulatory mechanisms is crucial for understanding the biological functions of sirtuins and development of potential therapeutics. In particular, SIRT1 has emerged as an attractive therapeutic target, and the search for SIRT1-activating compounds (STACs) has been actively pursued. However, the effectiveness of a class of reported STACs (represented by resveratrol) as direct SIRT1 activators is under debate due to the complication involving the use of fluorogenic substrates in in vitro assays. Future efforts of SIRT1-based therapeutics necessitate the dissection of the molecular mechanism of SIRT1 stimulation. We solved the structure of SIRT1 in complex with resveratrol and a 7-amino-4-methylcoumarin (AMC)-containing peptide. The structure reveals the presence of three resveratrol molecules, two of which mediate the interaction between the AMC peptide and the NTD of SIRT1. The two NTD-bound resveratrol molecules are principally responsible for promoting tighter binding between SIRT1 and the peptide and the stimulation of SIRT1 activity. The structural information provides valuable insights into regulation of SIRT1 activity and should benefit the development of authentic SIRT1 activators.

Structural transitions of centromeric chromatin regulate the cell cycle-dependent recruitment of CENP-N.

Specific recognition of centromere-specific histone variant CENP-A-containing chromatin by CENP-N is an essential process in the assembly of the kinetochore complex at centromeres prior to mammalian cell division. However, the mechanisms of CENP-N recruitment to centromeres/kinetochores remain unknown. Here, we show that a CENP-A-specific RG loop (Arg80/Gly81) plays an essential and dual regulatory role in this process. The RG loop assists the formation of a compact "ladder-like" structure of CENP-A chromatin, concealing the loop and thus impairing its role in recruiting CENP-N. Upon G1/S-phase transition, however, centromeric chromatin switches from the compact to an open state, enabling the now exposed RG loop to recruit CENP-N prior to cell division. Our results provide the first insights into the mechanisms by which the recruitment of CENP-N is regulated by the structural transitions between compaction and relaxation of centromeric chromatin during the cell cycle.

MP Allosterically Activates AMPK to Enhance ABCA1 Stability by Retarding the Calpain-Mediated Degradation Pathway.

It is widely recognized that macrophage cholesterol efflux mediated by the ATP-binding cassette transporter A1 (ABCA1) constitutes the initial and rate-limiting step of reverse cholesterol transport (RCT), displaying a negative correlation with the development of atherosclerosis. Although the transcriptional regulation of ABCA1 has been extensively studied in previous research, the impact of post-translational regulation on its expression remains to be elucidated. In this study, we report an AMP-activated protein kinase (AMPK) agonist called ((2R,3S,4R,5R)-3,4-dihydroxy-5-(6-((3-hydroxyphenyl) amino)-9H-purin-9-yl) tetrahydrofuran-2-yl) methyl dihydrogen phosphate (MP), which enhances ABCA1 expression through post-translational regulation rather than transcriptional regulation. By integrating the findings of multiple experiments, it is confirmed that MP directly binds to AMPK with a moderate binding affinity, subsequently triggering its allosteric activation. Further investigations conducted on macrophages unveil a novel mechanism through which MP modulates ABCA1 expression. Specifically, MP downregulates the Cav1.2 channel to obstruct the influx of extracellular Ca2+, thereby diminishing intracellular Ca2+ levels, suppressing calcium-activated calpain activity, and reducing the interaction strength between calpain and ABCA1. This cascade of events culminates in the deceleration of calpain-mediated degradation of ABCA1. In conclusion, MP emerges as a potentially promising candidate compound for developing agents aimed at enhancing ABCA1 stability and boosting cellular cholesterol efflux and RCT.

Cordycepin alleviated metabolic inflammation in Western diet-fed mice by targeting intestinal barrier integrity and intestinal flora.

Metabolic inflammation is a crucial factor in the pathogenesis of obesity and promotes related complications. Accumulating evidence has indicated that regulating intestinal integrity and the gut microbiota may be new treatment strategies for metabolic inflammation and obesity. Cordycepin has been reported to improve obesity, but the mechanism is not yet clear. Here, we showed that cordycepin considerably alleviated systemic inflammation while reducing body weight gain and metabolic disorders in Western diet (WD)-fed mice. Further investigations showed that cordycepin significantly ameliorated WD-induced damage to the intestinal barrier and decreased the leakage of lipopolysaccharide (LPS) into the blood in mice by suppressing intestinal inflammation, oxidative stress damage, and decreasing intestinal epithelial cell apoptosis and pyroptosis. In addition, by using metagenomic sequencing, we found that cordycepin could also regulate the homeostasis of intestinal flora, including selectively increasing the abundance of Akkermansia muciniphila and reducing the production of fecal LPS. Besides, we demonstrated that the intestinal flora partially mediated the beneficial effects of cordycepin on improving intestinal barrier function, and obesity-related symptoms in WD-fed mice by a fecal microbiota transplantation experiment. Hence, our findings provided new insights into the role of cordycepin in improving metabolic inflammation and obesity from the perspective of regulating the intestinal barrier function and intestinal flora, and further provided data support for the utility of cordycepin in the treatment of obesity and its complications.