Biology subjects

Deng, Z.

Publications and source records attributed to Deng, Z..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Discovery of the First-in-class G9a/GLP PROTAC Degrader

Aberrantly expressed lysine methyltransferases G9a and GLP, which catalyze mono- and di-methylation of histone H3 lysine 9 (H3K9), have been implicated in numerous cancers. Recent studies have uncovered both catalytic and non-catalytic oncogenic functions of G9a/GLP. As such, G9a/GLP catalytic inhibitors have displayed limited anticancer activity. Here, we report the discovery of the first-in-class G9a/GLP proteolysis targeting chimera (PROTAC) degrader, 10 (MS8709), as a potential anticancer therapeutic. 10 induces G9a/GLP degradation in a concentration-, time, and ubiquitin-proteasome system (UPS)-dependent manner, does not alter the mRNA expression of G9a/GLP and is selective for G9a/GLP over other methyltransferases. Moreover, 10 displays superior cell growth inhibition to the parent G9a/GLP inhibitor UNC0642 in prostate, leukemia, and lung cancer cells and has suitable mouse pharmacokinetic properties for in vivo efficacy studies. Overall, 10 is a valuable chemical biology tool to further investigate the functions of G9a/GLP and a potential therapeutic for treating G9a/GLP-dependent cancers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/582210v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1b3c923org.highwire.dtl.DTLVardef@5a22f0org.highwire.dtl.DTLVardef@1abbabeorg.highwire.dtl.DTLVardef@1711f29_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Machine learning identifies cell-free DNA 5-hydroxymethylation biomarkers that detect occult colorectal cancer in PLCO Screening Trial subjects

BackgroundColorectal cancer (CRC) is a leading cause of cancer-related mortality, and CRC detection through screening improves survival rates. A promising avenue to improve patient screening compliance is the development of minimally-invasive liquid biopsy assays that target CRC biomarkers on circulating cell-free DNA (cfDNA) in peripheral plasma. In this report, we identify cfDNA biomarker candidate genes bearing the epigenetic mark 5-hydroxymethylcytosine (5hmC) that diagnose occult CRC up to 36 months prior to clinical diagnosis using the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial samples. MethodsArchived PLCO Trial plasma samples containing cfDNA were obtained from the National Cancer Institute (NCI) biorepositories. Study subjects included those who were diagnosed with CRC within 36 months of blood collection (i.e., case, n = 201) and those who were not diagnosed with any cancer during an average of 16.3 years of follow-up (i.e., controls, n = 402). Following the extraction of 3 - 8 ng cfDNA from less than 300 microliters plasma, we employed the sensitive 5hmC-Seal chemical labeling approach, followed by next-generation sequencing (NGS). We then conducted association studies and machine-learning modeling to analyze the genome-wide 5hmC profiles within training and validation groups that were randomly selected at a 2:1 ratio. ResultsDespite the technical challenges associated with the PLCO samples (e.g., limited plasma volumes, low cfDNA amounts, and long archival times), robust genome-wide 5hmC profiles were successfully obtained from these samples. Association analyses using the Cox proportional hazards models suggested several epigenetic pathways relevant to CRC development distinguishing cases from controls. A weighted Cox model, comprised of 32-associated gene bodies, showed predictive detection value for CRC as early as 24-36 months prior to overt tumor presentation, and a trend for increased predictive power was observed for blood samples collected closer to CRC diagnosis. Notably, the 5hmC-based predictive model showed comparable performance regardless of sex and self-reported race/ethnicity, and significantly outperformed risk factors such as age and obesity according to BMI (body mass index). Additionally, further improvement of predictive performance was achieved by combining the 5hmC-based model and risk factors for CRC. ConclusionsAn assay of 5hmC epigenetic signals on cfDNA revealed candidate biomarkers with the potential to predict CRC occurrence despite the absence of clinical symptoms or the availability of effective predictors. Developing a minimally-invasive clinical assay that detects 5hmC-modified biomarkers holds promise for improving early CRC detection and ultimately patient survival through higher compliance screening and earlier intervention. Future investigation to expand this strategy to prospectively collected samples is warranted.

genomics↗

bioRxiv2024

Activated STING in the thymus alters T cell development and selection leading to autoimmunity

Classifying systemic inflammatory disorders as autoinflammatory or autoimmune provides insight into disease pathogenesis and whether treatment should target innate molecules and their signaling pathways or the adaptive immune response. COPA syndrome is a monogenic disorder of immune dysregulation that leads to interstitial lung disease and high-titer autoantibodies. Studies show constitutive activation of the innate immune molecule STING is centrally involved in disease. However, the mechanisms by which STING results in loss of T cell tolerance and autoimmunity in COPA syndrome or more common autoimmune diseases is not understood. Using CopaE241K/+ mice, we uncovered a functional role for STING in the thymus. Single cell data of human thymus demonstrates STING is highly expressed in medullary thymic epithelial cells (mTECs) involved in processing and presenting self-antigens to thymocytes. In CopaE241K/+ mice, activated STING in mTECs triggered interferon signaling, impaired macroautophagy and caused a defect in negative selection of T cells. Wild-type mice given a systemic STING agonist phenocopied the selection defect and showed enhanced thymic escape of a T cell clone targeting a self-antigen also expressed in melanoma. Our work demonstrates STING activation in TECs shapes the T cell repertoire and contributes to autoimmunity, findings important for settings that activate thymic STING. SummaryActivation of STING in thymic epithelial cells shifts the T cell repertoire to promote autoimmunity providing a new mechanistic link between innate and adaptive immunity.

immunology↗

bioRxiv2024

Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168

AbstractsThe DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, plays a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent Lys13 and Lys15 sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to ubiquitinate H2AK13/15 site-specifically has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c[~]Ub in complex with nucleosomes. Here, we developed mechanism-based chemical trapping strategies and determined the cryo-EM structures of the RNF168/UbcH5c-Ub/NCP complex captured in transient H2AK13/15 monoubiquitination and adjacent dual-monoubiquitination reactions. Our structural analysis revealed that RNF168 stably binds to the nucleosomal H2A-H2B acidic patch through a basic helix with multiple interactions, which positions the UbcH5c active centre directly over the H2A N-terminus, providing a "helix-anchoring" mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the "compass-binding" mode of dimeric E3 ligases. Furthermore, our chemically synthesized ubiquitinated histones have enabled the elucidation of the efficiency of Ub installation and the interplay between the initial and subsequent Ub modifications on the adjacent H2A K13 and K15 sites. Overall, our work not only provides structural snapshots of H2A K13/K15 site-specific monoubiquitination and adjacent dual-monoubiquitination, but also offers a near-atomic resolution structural framework for understanding how pathogenic mutations or physiological modifications affect the molecular function of RNF168 in H2A K13/15 ubiquitination.

biochemistry↗

bioRxiv2023

Aberrant connective tissue sheath contraction drives premature hair follicle regression by inducing progenitor cell depletion in androgenetic alopecia

Androgenetic alopecia (AGA) is characterized by progressive miniaturization of hair, forming a distinctive patterned baldness in the scalp; yet, the mechanisms for hair miniaturization in this disease remain largely unknown. Here by single-cell transcriptome analysis, we describe a concise single-cell atlas, and identify the early changes in cell subpopulations, hair follicle (HF) stem cell fate determination and cell-cell communications in AGA anagen HF units. Thereinto, apoptotic loss of HF progenitor cells is significantly increased, correlated with HF miniaturization in AGA. Mechanistically, enhanced contraction of connective tissue sheath (CTS) activates the mechanosensitive channel PIEZO1, which triggers ectopic apoptosis of progenitor cells in human anagen HFs. Continuous CTS contraction during AGA causes long-term loss of progenitor cells via inducing persistent ectopic apoptosis through PIEZO1, eventually leading to premature hair regression. Most importantly, we show that targeting CTS contraction by ML-7, a selective myosin light chain kinase (MLCK) inhibitor, can obviously improve the growth of HFs from balding scalps of AGA patients. Our study reveals the cellular hierarchies and identifies CTS with increased muscle contraction activity as a driver of premature hair regression in AGA, highlighting CTS surrounding human HF as the therapeutic target for treating this disorder.

pathology↗

bioRxiv2023

Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images

Stereo-seq is a cutting-edge technique for spatially resolved transcriptomics that combines subcellular resolution with centimeter-level field-of-view, serving as a technical foundation for analyzing large tissues at the single-cell level. Our previous work presents the first one-stop software that utilizes cell nuclei staining images and statistical methods to generate high-confidence single-cell spatial gene expression profiles for Stereo-seq data. With recent advancements in Stereo-seq technology, it is possible to acquire cell boundary information, such as cell membrane/wall staining images. To take advantage of this progress, we update our software to a new version, named STCellbin, which utilizes the cell nuclei staining images as a bridge to align cell membrane/wall staining images with spatial gene expression maps. By employing an advanced cell segmentation technique, accurate cell boundaries can be obtained, leading to more reliable single-cell spatial gene expression profiles. Experimental results verify that STCellbin can be applied on the mouse liver (cell membranes) and Arabidopsis seed (cell walls) datasets and outperforms other competitive methods. The improved capability of capturing single cell gene expression profiles by this update results in a deeper understanding of the contribution of single cell phenotypes to tissue biology. Availability & ImplementationThe source code of STCellbin is available at https://github.com/STOmics/STCellbin.

bioinformatics↗

bioRxiv2023

Trigeminal nerve direct current stimulation causes sustained increase in neural activity in the rat hippocampus

Transcranial direct current stimulation (tDCS) is a noninvasive neuromodulation method that can modulate many brain functions including learning and memory. Recent evidence suggests that tDCS memory effects may be caused by co-stimulation of scalp nerves such as the trigeminal nerve (TN), and not the electric field in the brain. The TN gives input to brainstem nuclei, including the locus coeruleus that controls noradrenaline release across brain regions, including hippocampus. However, the effects of TN direct current stimulation (TN-DCS) are currently not well understood. In this study we hypothesized that TN-DCS manipulates hippocampal activity via an LC-noradrenergic bottom-up pathway. We recorded neural activity in rat hippocampus using multichannel silicon probes. We applied 3 minutes of 0.25 mA or 1 mA TN-DCS, monitored hippocampal activity for up to 1 hour and calculated spikes-rate and spike-field coherence metrics. Subcutaneous injections of xylocaine were used to block TN and intraperitoneal injection of clonidine to block the LC pathway. We found that 1 mA TN-DCS caused a significant increase in hippocampal spike-rate lasting 45 minutes in addition to significant changes in spike-field coherence, while 0.25 mA TN-DCS did not. TN blockage prevented spike-rate increases, confirming effects were not caused by the electric field in the brain. When 1 mA TN-DCS was delivered during clonidine blockage no increase in spike-rate was observed, suggesting an important role for the LC-noradrenergic pathway. These results provide a neural basis to support a tDCS TN co-stimulation mechanism. TN-DCS emerges as an important tool to potentially modulate learning and memory. HighlightsO_LITrigeminal nerve direct current stimulation (TN-DCS) boosts hippocampal spike rates C_LIO_LITN-DCS alters spike-field coherence in theta and gamma bands across the hippocampus. C_LIO_LIBlockade experiments indicate that TN-DCS modulated hippocampal activity via the LC-noradrenergic pathway. C_LIO_LITN-DCS emerges as a potential tool for memory manipulation. C_LI Figure Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/571341v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@d60a69org.highwire.dtl.DTLVardef@4598daorg.highwire.dtl.DTLVardef@1363f89org.highwire.dtl.DTLVardef@856b2e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Tracing cellular dynamic changes across conditions, time, and space is crucial for understanding the molecular mechanisms underlying complex biological systems. However, integrating multi-sample data in a unified and flexible way to explore cellular heterogeneity remains a major challenge. Here, we present Stereopy, a flexible and versatile framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this flexible framework, we have developed three key components: a multi-sample tailored data container, a scope controller, and an analysis transformer. Furthermore, Stereopy showcases three transformative applications supported by pivotal algorithms. Firstly, the multi-sample cell community detection (CCD) algorithm introduces an innovative capability to detect specific cell communities and identify genes responsible for pathological changes in comparable datasets. Secondly, the spatially resolved temporal gene pattern inference (TGPI) algorithm represents a notable advancement in detecting important spatiotemporal gene patterns while concurrently considering spatial and temporal features, which enhances the identification of important genes, domains and regulatory factors closely associated with temporal datasets. Finally, the 3D niche-based regulation inference tool, named NicheReg3D, reconstructs the 3D cell niches to enable the inference of cell-gene interaction network within the spatial texture, thus bridging intercellular communications and intracellular regulations to unravel the intricate regulatory mechanisms that govern cellular behavior. Overall, Stereopy serves as both a bioinformatics toolbox and an extensible framework that provides researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.

bioinformatics↗

bioRxiv2023

Glycodiversification of gentamicins through in vivo glycosyltransferase swapping enabled the creation of novel hybrid aminoglycoside antibiotics with potent activity and low ototoxicity

Aminoglycosides (AGs) are a class of potent antibiotics with a broad spectrum of activity. However, their use is limited by safety concerns associated with nephrotoxicity and ototoxicity, as well as drug resistance. To address these issues, semi-synthetic approaches for modifying natural AGs have successfully generated new generations of AGs, however, with limited types of modification due to significant challenges in synthesis. This study explores a novel approach that harness the bacterial biosynthetic machinery of gentamicins and kanamycins to create hybrid AGs, installing extensive natural modifications from gentamicins onto kanamycins. This was achieved by glycodiversification of gentamicins via swapping the glycosyltransferase (GT) in their producer with the GT from kanamycins biosynthetic pathway and resulted in the creation of a series of novel AGs with combined structural features of two, therefore referred to as genkamicins (GKs). The manipulation of the hybrid metabolic pathway enabled the target accumulation of different GK species and the successful isolation and characterization of six GK components. These compounds display retained antimicrobial activity against a panel of World Health Organization (WHO) critical priority pathogens, and GK-C2a, in particular, demonstrates low ototoxicity compared to clinical drugs in zebrafish embryos. This study provides a new strategy for diversifying the structure of AGs and a potential avenue for developing less toxic AG drugs to combat infectious diseases.

synthetic biology↗

bioRxiv2023

Alteration in Gut Microbiome and Intestinal Barrier Function caused by Efavirenz versus Dolutegravir Treatments in Mice

Dolutegravir (DTG) is replacing efavirenz (EFV) as first-line antiretroviral therapy because of its better tolerance. However, DTG cause similar, but milder, gastrointestinal and neurological side effects as EFV does. We speculated that impaired gut barrier function contributes to their side effects. For this purpose, the mice were intragastrically administered EFV, DTG, or vehicle for 60 consecutive days. The plasma levels of FITC-dextran were determined to evaluate gut barrier integrity. Colonic contents were collected for 16S rRNA sequencing. Adipose, liver, ileum, and colon tissues were collected for pathological examination, and intestinal zona occludens-1 (ZO-1) immunofluorescence staining and goblet cell staining were performed. We found that EFV significantly retarded body weight gain, decreased glucose uptake, and caused lipodystrophy and hepatocyte necrosis. EFV also decreased species richness of gut microbiota, increased Verrucomicrobia and Proteobacteria, and decreased Patescibacteria and Cyanobacteria. Moreover, it caused crypt damage, goblet cell loss, reduced ZO-1 expression, impaired gut barrier function, and suppressed expressions of Pdha1 and Ndufv1. Interestingly, DTG impaired barrier function similar to EFV, but the impairment was milder. DTC also inhibited MPC1, MPC2, and Pdha1 expression. Our results suggest a link between abnormal energy metabolism, impaired gut barrier integrity and side effects of EFV and DTG.

immunology↗

bioRxiv2023

Engineered dsRNA-protein nanoparticles for effective long-distance transport, delivery and gene silencing in plants

Long-distance transport of exogenous biologically active RNA molecules in higher plants has not been reported. Here, we report that cationized bovine serum albumin (cBSA) avidly binds double-stranded beta-glucuronidase RNA (dsGUS RNA) to form nucleic acid-protein nanocomplexes. Using tobacco and poplar plants, we have shown effective uptake and long-distance transport of cBSA/dsGUS RNA nanocomplexes from basal ends of leaf petioles to leaf blades as well as from basal ends of shoots to their apexes and apical leaves. We have further demonstrated that the cBSA/dsGUS RNA nanocomplexes are highly effective in silencing both conditionally inducible DR5-GUS gene and constitutively active 35S-GUS gene in leaf, shoot and shoot meristem tissues. This cBSA/dsRNA delivery technology may provide a convenient, fast, and inexpensive tool for characterizing gene functions in plants, and potentially for in planta gene-editing.

molecular biology↗

bioRxiv2023

GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model

Deciphering the universal gene regulatory mechanisms in diverse organisms holds great potential to advance our knowledge of fundamental life process and facilitate research on clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms, resulting in limited collection and integration of complex features on various cell types across species. Recent breakthroughs in single-cell sequencing and advancements in deep learning techniques present an unprecedented opportunity to tackle this challenge. In this study, we developed GeneCompass, the first knowledge-informed, cross-species foundation model pre-trained on an extensive dataset of over 120 million single-cell transcriptomes from human and mouse. During pre-training, GeneCompass effectively integrates four types of biological prior knowledge to enhance the understanding of gene regulatory mechanisms in a self-supervised manner. Fine-tuning towards multiple downstream tasks, GeneCompass outperforms competing state-of-the-art models in multiple tasks on single species and unlocks new realms of cross-species biological investigation. Overall, GeneCompass marks a milestone in advancing knowledge of universal gene regulatory mechanisms and accelerating the discovery of key cell fate regulators and candidate targets for drug development.

bioinformatics↗

bioRxiv2023

TreeProfiler: A command-line tool for computing and visualizing phylogenetic profiles against large trees

Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infer gene function from co-evolutionary patterns (phylogenetic profiling), reconstruct ancestral states, and uncover ecological associations. However, existing profiling tools are typically tailored to specific use cases, have limited scalability for large datasets, and lack robust methods to aggregate or summarize traits at internal tree nodes. Here, we present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes. TreeProfiler supports the profiling of custom continuous and discrete traits, as well as ancestral character reconstruction and phylogenetic signal tests. It also integrates commonly used genomic features, including multiple sequence alignments, protein domain architectures, and functional annotations. We demonstrate TreeProfilers utility beyond traditional phylogenetic profiling by analyzing functional diversification and domain architectures within the pyruvate flavodoxin/ferredoxin oxidoreductase gene family (13,297 genes), and by profiling the relative abundance of 124,295 bacterial and archaeal species across 51 biomes. TreeProfiler is open-source and freely available at https://github.com/compgenomicslab/TreeProfiler.

bioinformatics↗

bioRxiv2023

Proteonano: a novel deep proteomics platform with 1000-plex profiling capacity and picogram sensitivity and its application in diabetic kidney disease

The development of blood-based multi-biomarker panels for screening diabetic patients, and as an easy-to-access tool for identifying individuals at greatest risk of developing diabetic kidney disease (DKD) and its progression, is essential. However, conventional blood biomarker-based methodologies (e.g. clinical tests and ELISA) are unable to predict DKD progression with high sensitivity and specificity. To overcome these challenges, we developed a deep, untargeted plasma proteome profiling technology (Proteonano platform) to identify potential multiple protein biomarkers involved in DKD progression. The Proteonano technology is an affinity selective mass spectrometric platform that comprises nanoparticle-based affinity binders (nanobinders) for low abundant protein enrichment, automated workflow for parallel sample preparation, and machine learning empowered bioinformatic software for data analysis. Using the Proteonano platform, we performed untargeted proteomics on 75 subjects (DKD progressors, n = 30; DKD non-progressors, n = 45) and identified an average of 953 {+/-} 80 (AVG {+/-} SD) protein groups, with a wide dynamic range of 8 orders of magnitude (with the lowest concentration down to 3.00 pg/mL). Among these, 38 proteins were differentially expressed between DKD progressors relative to non-progressors, and the predictive power for these proteins were assessed. Further, we performed random forest and LASSO analyses for additional variable selection. Variables selected by these approaches were assessed by Akaike information criterion method followed by ROC analysis, which identified a combination of multiple proteins (including VWF, PTGDS, B2M, BT3A2, and LCAT) that showed excellent predictive power over current methods, with an area under the curve value up to 0.97. Some of these plasma proteins are not previously recognized in the context of DKD progression, suggesting they are novel biomarkers. Our studies pave the way to develop multi-biomarker panels for DKD progression management. This study suggests that the Proteonano technology platform reported here can be employed as an established workflow enabling untargeted deep proteomic analysis to identify highly discriminative biomarkers for precise medicine.

bioinformatics↗

bioRxiv2023

Structural Basis of Streptomyces Antibiotic Regulatory Proteins Activating Transcription

Streptomycetes are renowned antibiotic producers, with Streptomyces antibiotic regulatory proteins (SARPs) acting as activators for antibiotic biosynthesis. However, the precise mechanism underlying SARPs transcriptional activation remains elusive. Here, we used cryo-electron microscopy (cryo-EM) to unravel the interplay between SARP, DNA, and RNA polymerase (RNAP) during transcriptional activation. The SARP domain of Streptomyces coelicolor AfsR (SAS) forms a side-by-side dimer contacting the afs box centered at -29.5 relative to the transcription start site. The upstream protomer binds to the direct repeat encompassing the -35 element while the {sigma}HrdB region 4 (R4) is positioned on top of both protomers, causing the removal of R4 from the major groove of the -35 element. Both SAS protomers establish interactions with C-terminal domain of one RNAP subunits, while specific regions of the RNAP {beta} flap tip helix and {beta} zinc-binding domain also engage with SAS. Key interfacial residues accounting for transcriptional activation were confirmed by mutational studies and in vitro transcriptional assays. Overall, our results present a detailed molecular view of how SARPs serve to activate transcription.

molecular biology↗

bioRxiv2023

Large-scale population genomics of Malayan pangolins reveals deep diversification and a new species

BackgroundArchipelagos and oceanic islands often present high percentage of endemism due to rapid speciation. The Malayan pangolin is a species distributing at both mainland (southern Yunnan, China) and oceanic islands via Malayan peninsula, which may result in deep differentiation among populations. In-depth investigation of population structure and genetic consequences for such species is of vital importance for their protection and conservation, practically for the critically endangered Malayan pangolin that is suffering from poaching, illegal trade, and habitat loss. ResultsHere we carried out a large-scale population genomic analysis for Malayan pangolins, and revealed three highly distinct genetic populations in this species, two of which are now being reported for the first time. Based on multiple lines of genomic and morphological evidence, we postulate the existence of a new pangolin species (Manis_1). Genetic diversity and recent inbreeding were both at a moderate level for both Malayan pangolins and Manis_1, but mainland Malayan pangolins presented relatively lower genetic diversity, higher inbreeding and fitness cost than island populations. ConclusionsWe found extremely deep and graded differentiation in Malayan pangolins, with two newly discovered genetic populations and a new pangolin species that is closely related to the Philippine pangolin than the typical Malayan pangolin, but a distant relative of the Indian pangolin. Anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins, but mainland Malayan pangolins should be paid more attention for conservation due to higher genetic risks than island populations.

genomics↗

bioRxiv2023

A Cryptic Basic Groove formed by Ubiquitin and Histone H3 Mediates the Selective Recognition of H2AK119Ub Nucleosomes by Synovial Sarcoma X Breakpoint 1 Protein

The cancer-specific fusion oncoprotein SS18-SSX1 disturbs chromatin accessibility by hijacking the BAF complex from the promoters and enhancers to the polycomb-repressed chromatin regions. This process relies on the selective recognition of H2AK119Ub nucleosomes by SSX1. However, the mechanism by which SSX1 selective recognition of H2AK119Ub nucleosomes in the absence of ubiquitin (Ub)-binding capacity remains unknown. Here we report the cryo-EM structure of SSX1 bound to H2AK119Ub nucleosomes at 3.1 [A] resolution. Combined in vitro biochemical and cellular assays revealed that the Ub recognition by SSX1 is unique and depends on a cryptic basic groove formed by H3 and the Ub motif on the H2AK119 site. Moreover, this unorthodox binding mode of SSX1 induces DNA unwrapping at the entry/exit sites. Together, our results describe a unique mode of site-specific ubiquitinated nucleosome recognition that underlies the specific hijacking of the BAF complex to polycomb regions by SS18-SSX1 in synovial sarcoma.

molecular biology↗

bioRxiv2023

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

BackgroundBlackberries (Rubus subgenus Rubus) are a major berry crop consumed globally for being a rich source of anthocyanins and antioxidants, and their unique flavor. However, breeding for fruit improvement in blackberry has been significantly hindered by the scarcity of genomic resources and the genetic complexity of traits. The blackberry genome has been particularly challenging to assemble, largely due to its polyploid nature. FindingsWe present the first chromosome-scale and haplotype-phased genome assembly for the cultivated primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The tetraploid genome assembly was generated using the Oxford Nanopore Technology (ONT) and Hi-C scaffolding, comprising 919 Mb placed on 27 pseudochromosomes with an N50 of 35.73 Mb. The assembly covers >92% of the genome length and contains over 98% of complete BUSCOs. Repetitive sequences constitute 57% of the assembly, with the long terminal repeats (LTR) being the most abundant class. A total of 87,968 protein-coding genes were predicted, of which, 82% were functionally annotated. Gene expression analyses identified candidate genes and transcription factors related to thornlessness in blackberries, including MYB16, lysine histidine transporters, PDR1, Caffeoyl-CoA, glycosylphosphatidylinositol-anchored lipid protein transfer 1, DRN, beta-ketoacyl reductase, and homocysteine S-methyltransferase 3. ConclusionsThe utility of this genome has been demonstrated in this study by identifying candidate genes related to thornlessness in blackberry. Resequencing of tetraploid blackberry cultivars/selections with different horticultural characteristics revealed genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome will serve as a valuable resource to accelerate genetic analysis and breeding of this important berry crop, enabling the development of improved varieties with enhanced traits.

plant biology↗