Biology subjects

Song, B.

Publications and source records attributed to Song, B..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

MIWI arginines orchestrate generation of functional pachytene piRNAs and spermiogenesis

N-terminal arginine (NTR) methylation is a conserved feature of PIWI proteins, which are central components of the PIWI-interacting RNA (piRNA) pathway. The significance and precise function of PIWI NTR methylation in mammals remains unknown. In mice, PIWI NTRs bind Tudor domain containing proteins (TDRDs) that have essential roles in piRNA biogenesis and the formation of the chromatoid body. Using mouse MIWI (PIWIL1) as paradigm, we demonstrate that the NTRs are essential for spermatogenesis through the regulation of transposons and gene expression. Surprisingly, the loss of TDRD5 and TDRKH interaction with MIWI results in defective piRNA amplification, rather than an expected failure of piRNA biogenesis. We find that piRNA amplification is necessary for both transposon control and for sustaining levels of select, nonconserved, pachytene piRNAs that target specific mRNAs required for spermatogenesis. Our findings support the notion that the vast majority of pachytene piRNAs are dispensable, acting as autonomous genetic elements that rely for propagation on MIWI piRNA amplification. MIWI-NTRs also mediate interactions with TDRD6 that are necessary for chromatoid body compaction. Furthermore, MIWI-NTRs promote stabilization of spermiogenic transcripts that drive nuclear compaction, which is essential for sperm formation. In summary, the NTRs underpin the diversification of MIWI protein function. Key pointsO_LIMIWI-NTRs coordinate interactions with TDRDs required for piRNA biogenesis to sustain piRNA amplification C_LIO_LIMIWI-NTRs are necessary for both transposon control and for sustaining levels of select pachytene piRNAs that target specific mRNAs required for spermiogenesis C_LIO_LIMIWI-NTRs mediate interactions with TDRD6 to compact the Chromatoid Body C_LIO_LIMIWI-NTRs underlie stabilization of spermiogenic transcripts that drive nuclear compaction, which is essential for sperm formation C_LI

molecular biology↗

bioRxiv2023

Decoding Heterogenous Single-cell Perturbation Responses

Understanding diverse responses of individual cells to the same perturbation is central to many biological and biomedical problems. Current methods, however, do not precisely quantify the strength of perturbation responses and, more importantly, reveal new biological insights from heterogeneity in responses. Here we introduce the perturbation-response score (PS), based on constrained quadratic optimization, to quantify diverse perturbation responses at a single-cell level. Applied to single-cell transcriptomes of large-scale genetic perturbation datasets (e.g., Perturb-seq), PS outperforms existing methods for quantifying partial gene perturbation responses. In addition, PS presents two major advances. First, PS enables large-scale, single-cell-resolution dosage analysis of perturbation, without the need to titrate perturbation strength. By analyzing the dose-response patterns of over 2,000 essential genes in Perturb-seq, we identify two distinct patterns, depending on whether a moderate reduction in their expression induces strong downstream expression alterations. Second, PS identifies intrinsic and extrinsic biological determinants of perturbation responses. We demonstrate the application of PS in contexts such as T cell stimulation, latent HIV-1 expression, and pancreatic cell differentiation. Notably, PS unveiled a previously unrecognized, cell-type-specific role of coiled-coil domain containing 6 (CCDC6) in guiding liver and pancreatic lineage decisions, where CCDC6 knockouts drive the endoderm cell differentiation towards liver lineage, rather than pancreatic lineage. The PS approach provides an innovative method for dose-to-function analysis and will enable new biological discoveries from single-cell perturbation datasets. One sentence summaryWe present a method to quantify diverse perturbation responses and discover novel biological insights in single-cell perturbation datasets.

bioinformatics↗

bioRxiv2023

Transposable element abundance subtly contributes to lower fitness in maize

Transposable elements (TEs) have long been shown to have deleterious effects on the survival and reproduction of their host organism. As TEs are mobile DNA that jump to new positions, this deleterious cost can occur directly, by inserting into genes and regulatory sequences. Classical population genetic theory suggests copy-number dependent selection against TEs is necessary to prevent TEs from expanding so much they take over a genome. Such models have been difficult to interpret when applied to large genomes like maize, where there are hundreds of thousands of TE insertions that collectively make up 85% of the genome. Here, we use nearly 5000 inbred lines from maize mapping populations and a pan-genomic imputation approach to measure TE content. Segregating TE content gives rise to 100 Mb differences between individuals, and populations often show transgressive segregation in TE content. We use replicated phenotypes measured in hybrids across numerous years and environments to empirically measure the fitness costs of TEs. For an annual plant like maize, grain yield is not only a key agronomic phenotype, but also a direct measure of reproductive output. We find weak negative effects of TE accumulation on grain yield, nearing the limit of the efficacy of natural selection in maize. This results in a loss of one kernel ({approx}0.1% of average per-plant yield) for every additional 14 Mb of TE content. This deleterious load is enriched in TEs within 1 kilobase of genes and young TE insertions. Together, we provide rare empirical measurements of the fitness costs of TEs, and suggest that the TEs we see today in the genome have been filtered by selection against their deleterious consequences on maize fitness.

evolutionary biology↗

bioRxiv2023

Enhancement of Protein Stability by Quenching Millisecond Conformational Dynamics

Protein folding may involve folding intermediates. Ubiquitin (Ub) is a 76-residue small protein essential in post-translational modification and cell signaling. Ub is also a model system of protein folding. Previous studies have indicated the involvement of a folding intermediate, as Ub C-terminal residues, including strand {beta}5, only dock correctly at a later stage. The natively folded Ub undergoes conformational dynamics over a vast range of timescales. At the millisecond timescale, Ub transiently digresses to a C-terminally retracted state, which is extremely rare and has only been recently identified at an elevated temperature. Herein through a conjoint use of NMR, MS, and MD simulations, we have established a link between Ub millisecond dynamics and protein stability. Among the alanine mutations that have been systematically introduced to the hydrophobic residues in {beta}5, L67A and L69A elevate the population of the retracted state and enhance conformational interconversion, which facilitates the undocking of {beta}5 and the exposure of protein hydrophobic core. Conversely, L71A and L73A mutations decrease the population of the retracted state and quench millisecond dynamics, which causes a significant enhancement of protein stability. As such, the transition state of Ub millisecond dynamics is the much sought-after folding intermediate, whereas C-terminal mutations alleviate the dependence on this intermediate and reduce the unfolding to an all-or-none process. Though having a negative impact on protein stability, Ub millisecond dynamics likely facilitate proper protein turnover and allow the fulfillment of its biological function.

biophysics↗

bioRxiv2023

Ca2+-sensing receptor regulates neuronal excitability via Kv7 channel and Gi/o protein signalling

Neuropathic pain, a debilitating condition with unmet medical needs, can be charactarised as hyperexcitability of nociceptive neurons caused by dysfunction of ion channels. Voltage-gated potassium channel type 7 (Kv7), responsible for maintaining neuronal resting membrane potential and thus neuronal exitability, resides under tight control of G protein-coupled receptors (GPCR). Calcium-sensing receptor (CaSR) is a GPCR that is known to regulate activity of numerous ion channels, but whether CaSR could control Kv7 channel function has been unexplored until now. Our results demonstrate that CaSR is expressed in recombinant cell models, human induced pluripotent stem cell (hiPSC)-derived nociceptive-like neurons and mouse dorsal root ganglia neurons, and its activation induced depolarisation via Kv7.2/7.3 channel inhibition. The CaSR-Kv7.2/7.3 channel crosslink was mediated via the Gi/o protein/adenylate cyclase/cyclic adenosine monophosphate/protein kinase A signalling cascade. Suppression of CaSR function rescued hiPSC-derived nociceptive-like neurons from algogenic cocktail-induced hyperexcitability. To conclude, this study demonstrates that CaSR-Kv7.2/7.3 channel crosslink via the Gi/o protein signalling pathway effectively regulates neuronal excitability, providing a feasible pharmacological target for neuronal hyperexcitability management in neuropathic pain.

physiology↗

bioRxiv2023

Histone deacetylase 3 plays a critical role in hypertension-induced kidney inflammation and fibrosis

Objective: Hypertension is a major cause of chronic kidney disease. The molecular mechanisms how hypertension causes kidney disease are not fully understood. In this study, we examined the functional role of histone deacetylase 3 (HDAC3) in the pathogenesis of hypertensive kidney disease. Approach and Results: Myeloid HDAC3 knockout mice were generated by crossing HDAC3f/f mice with LysM-Cre+/- mice. Both LysM-Cre-/-HDAC3f/f (HDAC3CON) mice and LysM-Cre+/+HDAC3f/f (HDAC3MKO) mice were subjected to uninephrectomy and treated with angiotensin II at 1.5 ug/kg/min or vehicle for 28 days. Blood pressure increased comparably in both HDAC3CON and HDAC3MKO mice following angiotensin II treatment. Compared with HDAC3CON mice, HDAC3MKO mice were protected from angiotensin II-induced kidney dysfunction and pathological injury and developed less proteinuria. Myeloid HDAC3 deficiency markedly attenuated the protein levels of fibronectin, collagen I, and ?-SMA in the kidney following angiotensin II treatment. Furthermore, HDAC3MKO mice accumulated significantly fewer myeloid fibroblasts and macrophages in the kidney after angiotensin II treatment. Myeloid HDAC3 deficiency significantly reduced the mRNA expression of proinflammatory molecules in the kidney following angiotensin II treatment. In cultured macrophages, knockdown of HDAC3 with shRNA suppressed proinflammatory molecule expression. Furthermore, knockdown of HDAC3 inhibited NF-kB p65 enrichment to IL-6 promoter. Conclusion: Our study identifies a critical role of myeloid HDAC3 in the regulation of hypertension-induced kidney inflammation and fibrosis. Targeting HDAC3 may represent a novel therapeutic strategy for hypertensive kidney disease.

pathology↗

bioRxiv2023

A toxic ankyrin cysteine protease effector RipBH of brown rot triggered autophagy-associated cell death

Potato brown rot, caused by Ralstonia solanacearum, is one of the most destructive diseases of potatoes. The pathogen could hide in the tuber, leading to the rotting tubers. However, few mechanisms of pathogenesis in tubers caused by brown rot were reported. Here, we identified a highly virulent type III effector RipBH, which is not only required for the pathogenesis of potato brown rot but also displays strong cell toxicity in yeast and tobacco. We found RipBH is a novel structural cysteine protease with a large ankyrin repeat domain that contains 10 ankyrin repeats, we named it as an ankyrin cysteine protease. Biochemical analysis showed that all the ankyrin repeats are required for virulence, and the first five ankyrin repeats are indispensable for auto-cleavage site recognition. Further analysis showed that RipBH triggered autophagy-associated cell death. The ankyrin cysteine protease effector existed extensively in plant and animal pathogens suggesting the ankyrin cysteine protease effectors are functionally essential for pathogen pathogenesis. Our study enhances our understanding of this type of cysteine protease and illustrates the pathogenesis of cysteine protease in potato brown rot.

microbiology↗

bioRxiv2023

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

BackgroundStructural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de-novo genome assemblies of 26 diverse inbred maize lines. ResultsWe generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both putative insertion and deletion events. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that, genome-wide, deletions of transposable elements account for more structural variation than insertions. These deletions are often large structural variants containing multiple transposable elements. ConclusionsCombined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.

genomics↗

bioRxiv2023

Comparison between Canine and Porcine Models of Chronic Deep Venous Thrombosis

Venous thromboembolism(VTE) refers to deep venous thrombosis(DVT) and pulmonary embolism(PE), which is a worldwide problem and has very high morbidity and mortality. The research of venous thrombosis involves pathogenesis, pathophysiology, and therapeutic attempt. Alternative experimental animal models have changed dramatically over the past 20 years, from small murine models to large ones. Larger animal models offer more options and are more consistent with human physiology. This article aims to induce chronic deep venous thrombosis in the left iliac vein in canine and porcine models and compare these two models. We think that feasible large animal models can better translate the results of therapeutic research into clinical application.

animal behavior and cognition↗

bioRxiv2023

The Effect of Electrical Resonance in Neurons upon the Instability of Electrical Nerve Stimulations

Repetitive electrical nerve stimulation can induce a long-lasting perturbation of the axons membrane potential, resulting in unstable stimulus-response relationships. Despite being observed in electrophysiology, the precise mechanisms underlying stimulus-induced instability is still an open question due to the lack of a proper theoretical model. This study proposes a new method based on a Circuit-Probability theory to reveal the interlinkages between the electrical resonance of neurons and the instability of neural response. Supported by in vivo investigations, this new model predicts several key characteristics of stimulus-induced instability and proposes a stimulation method to minimize the instability. This model provides a powerful tool to improve our understanding of the interaction between the external electric field and the complexity of the biophysical characteristics of axons.

neuroscience↗

bioRxiv2022

Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice

Schizophrenia disease mechanisms remain poorly understood, in large part due to a lack of valid animal models. Rare heterozygous loss-of-function mutations in GRIN2A, encoding a subunit of the NMDA (N-methyl-d-aspartate) receptor, greatly increase the risk of schizophrenia. By transcriptomic, proteomic, electroencephalogram (EEG) recording and behavioral analysis, we report that heterozygous Grin2a mutant mice show: (i) large-scale gene expression changes across multiple brain regions and in neuronal (excitatory and inhibitory) and non-neuronal cells (astrocytes, oligodendrocytes); (ii) evidence of reduced activity in prefrontal cortex and increased activity in hippocampus and striatum; (iii) elevated dopamine signaling in striatum; (iv) altered cholesterol biosynthesis in astrocytes; (v) reduction of glutamatergic receptor signalin g proteins in the synapse; (iv) heightened gamma oscillation power in EEG; (vi) aberrant locomotor behavioral pattern opposite of that induced by antipsychotic drugs. These findings reveal potential pathophysiologic mechanisms, provide support for both the "hypo-glutamate" and "hyper-dopamine" hypotheses of schizophrenia, and underscore the utility of Grin2a-deficient mice as a new genetic model of schizophrenia.

neuroscience↗

bioRxiv2022

Deep proteomics identifies shared molecular pathway alterations in synapses of schizophrenia and bipolar disorder patients and mouse model

Synaptic dysfunction is implicated in the pathophysiology of schizophrenia (SCZ) and bipolar disorder (BP). We used quantitative mass-spectrometry to carry out deep and unbiased profiling of the proteome of synapses purified from the dorsolateral prefrontal cortex of 35 cases of SCZ, 35 cases of BP, and 35 controls. Compared to controls, SCZ and BP synapses showed substantial and similar proteomic alterations. Network and gene set enrichment analyses revealed upregulation of proteins associated with autophagy and certain vesicle transport pathways, and downregulation of proteins related to synaptic, mitochondrial, and ribosomal function in the synapses of individuals with SCZ or BP. Some of the same pathways (e.g., upregulation of vesicle transport, downregulation of mitochondrial and ribosomal proteins) were similarly dysregulated in the synaptic proteome of mutant mice deficient in Akap11, a recently discovered shared risk gene for SCZ and BP. Our work provides novel biological insights into molecular dysfunction at the synapse in SCZ and BP and serves as a resource for understanding the pathophysiology of these debilitating neuropsychiatric disorders.

neuroscience↗

bioRxiv2022

Resilient anatomy and local microplasticity of na&iumlve and stress hematopoiesis

The bone marrow has an extraordinary capacity to adjust blood cell production to meet physiological demands in response to insults. The spatial organization of normal and stress responses is largely unknown due to the lack of methods to visualize most steps of blood production. Here we develop strategies to image multipotent hematopoiesis, megakaryopoiesis, erythropoiesis, and lymphopoiesis in mice. We combine these with imaging of myelopoiesis1 to define the anatomy of hematopoiesis in homeostasis, after acute insults, and during geriatric age. Blood production takes place via long-range migration of multipotent progenitors away from stem cells. Lineage-committed progenitors are then serially recruited to blood vessels where they contribute to lineage-specific microanatomical structures, composed of progenitors and immature cells, which function as production lines for mature blood cells. This anatomy is durable and resilient to insults as it was maintained after hemorrhage, acute bacterial infection, and with aging. Production lines enable hematopoietic plasticity as they differentially -and selectively-modulate their numbers and output in response to acute insults and then return to homeostasis. In geriatric mice the number of production lines is maintained, but their microanatomy becomes permanently remodeled in a cell- and lineage-specific manner indicating chronic anatomical adaptations to hematopoietic aging. Our studies uncover the sophisticated and durable anatomy of blood production -defined by distinct migratory behaviors depending on the maturation stage- and identify discrete microanatomical production lines that confer plasticity to hematopoiesis.

physiology↗

bioRxiv2022

Striosomes constrain locomotor vigor with respect to an innate valence differential

Survival demands that safe and unsafe contexts are met with different locomotor profiles, yet whether striatal microcircuitry links contextual valence to spontaneous locomotor vigor is unresolved. Here we test for striosome contributions to spontaneous locomotion using ablation, calcium imaging and chemogenetics in the context of a modified Light/Dark box test. We found that locomotor speed reflects the unlearned, external valence differential present in this test, and that striosomes gate valence-oriented speed selection. Our data suggest that striosomes dampen motor vigor associated with lesser valence, or elevated anxiety. HighlightsO_LIMice explore the light and dark zones in Light/Dark box with different walk speed C_LIO_LIStriosome ablation reduces restful slowing and elevates speed relative to zone C_LIO_LIMany striosome neurons exhibit light-zone preference and speed related activity C_LIO_LIStriosome enhancement slows mice and blunts zone discrimination by speed C_LI

neuroscience↗

bioRxiv2022

A Comparison of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

While experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. CyTOF data are dramatically different from scRNA-seq data in many aspects. This calls for the evaluation and development of computational methods specific for CyTOF data. Dimension reduction (DR) is one of the critical steps of single cell data analysis. Here, we benchmark the performances of 21 DR methods on 110 real and 425 synthetic CyTOF samples. We find that less well-known methods like SAUCIE, SQuaD-MDS, and scvis are the overall best performers. In particular, SAUCIE and scvis are well balanced, SQuaD-MDS excels at structure preservation, whereas UMAP has great downstream analysis performance. We also find that t- SNE (along with SQuad-MDS/t-SNE Hybrid) possesses the best local structure preservation. Nevertheless, there is a high level of complementarity between these tools, so the choice of method should depend on the underlying data structure and the analytical needs.

bioinformatics↗

bioRxiv2022

Mouse mutants in schizophrenia risk genes GRIN2A and AKAP11 show EEG abnormalities in common with schizophrenia patients

BACKGROUNDSchizophrenia is a heterogeneous psychiatric disorder with a strong genetic basis, whose etiology and pathophysiology remain poorly understood. Exome sequencing studies have uncovered rare, loss-of-function variants that greatly increase risk of schizophrenia [1], including loss-of-function mutations in GRIN2A (aka GluN2A or NR2A, encoding the NMDA receptor subunit 2A) and AKAP11 (A-Kinase Anchoring Protein 11). AKAP11 and GRIN2A mutations are also associated with bipolar disorder [2], and epilepsy and developmental delay/intellectual disorder [1, 3, 4], respectively. Accessible in both humans and rodents, electroencephalogram (EEG) recordings offer a window into brain activity and display abnormal features in schizophrenia patients. Does loss of Grin2a or Akap11 in mice also result in EEG abnormalities? METHODSWe monitored EEG in heterozygous and homozygous knockout Grin2a and Akap11 mutant mice compared with their wild-type littermates, at 3- and 6-months of age, across the sleep/wake cycle and during auditory stimulation protocols. RESULTSGrin2a and Akap11 mutants exhibited increased resting gamma power, attenuated 40-50 Hz auditory steady-state responses (ASSR), and reduced responses to unexpected auditory stimuli during mismatch negativity (MMN) tests. Sleep spindle density was reduced in a gene dose-dependent manner in Akap11 mutants, whereas Grin2a mutants showed increased sleep spindle density. CONCLUSIONSThe EEG phenotypes of Grin2a and Akap11 mutant mice show a variety of abnormal features that overlap considerably with human schizophrenia patients, reflecting systems-level changes caused by Grin2a and Akap11 deficiency. These neurophysiologic findings further substantiate Grin2a and Akap11 mutants as genetic models of schizophrenia and identify potential biomarkers for stratification of schizophrenia patients.

neuroscience↗

bioRxiv2022

A role for heritable transcriptomic variation in maize adaptation to temperate environments

Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression. While genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7,614 genes. Rare allele burden within genomic intervals with trans-eQTLs correlated with extremes of expression in target genes as previously reported for cis-eQTLs. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in phytohormone pathways, cell wall biosynthesis, lipid metabolism and stress response. Several genes involved in cell proliferation, flower development, DNA replication and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions.

bioinformatics↗

bioRxiv2022

m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues

As the most pervasive epigenetic marker present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform m6A-TSHub for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB: a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder: a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar: a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modification; and (4) m6A-CAVar: a database of 587,983 TCGA cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and genetic factor of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at: www.xjtlu.edu.cn/biologicalsciences/m6ats.

bioinformatics↗