Biology subjects

Ye, L.

Publications and source records attributed to Ye, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Transcription factor GLK2 regulates key steps of anthocyanin biosynthesis to antagonize photo-oxidative stress during greening of Arabidopsis seedlings

The greening of young seedling is light induced but vulnerable to photo-oxidative stress at the same time, due to the immature status of chloroplasts. Accumulation of anthocyanin is a protective response to high light, by absorbing excess energy and serving as antioxidant. In this work with Arabidopsis, we found that GARP family transcription factors GOLDEN2-LIKE 2 (GLK2), as a key regulator to chloroplast development, also plays an intensive role in regulating anthocyanin biosynthesis during seedling de-etiolation, especially under high light stress. We demonstrate that GLK2 positively regulates anthocyanin biosynthesis by directly activating the transcription of anthocyanin late biosynthetic genes (LBGs) as well as TRANSPARENT TESTA GLABRA 1 (TTG1) gene, which encodes a key component of the regulatory MYB-bHLH-WDR (MBW) complex (which also activates LBGs). Our data further show that GLK2 and MBW each could activate the expression of DFR gene (key LBG) independently, via distinct promoter regions. We therefore propose a multifaceted involvement of GLK2 in anthocyanin biosynthesis as an important protective measure for developing chloroplasts, against excessive light exposure during seedling photomorphogenesis.

plant biology↗

bioRxiv2023

Single-cell transcriptomic analyses reveal the cellular and genetic basis of aquatic locomotion in scyphozoan jellyfish

The authors have withdrawn their manuscript because the authors need to re-organize the data and writing. More experimental evidence from whole-mount ISH assay and RNAi assays will be added to support the viewpoints. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

ecology↗

bioRxiv2023

Brainstem Dbh+ Neurons Control Chronic Allergen-Induced Airway Hyperreactivity

Chronic exposure of the lung to irritants such as allergen is a primary cause of asthma characterized by exaggerated airway constriction, also called hyperreactivity, which can be life-threatening. Aside from immune cells, vagal sensory neurons are important for airway hyperreactivity 1-4. However, the identity and signature of the downstream nodes of this adaptive circuit remains poorly understood. Here we show that a single population of Dbh+neurons in the nucleus of the solitary tract (nTS) of the brainstem, and downstream neurons in the nucleus ambiguous (NA), are both necessary and sufficient for chronic allergen-induced airway hyperreactivity. We found that repeated exposures of mice to inhaled allergen activates nTS neurons in a mast cell-, interleukin 4 (IL-4)-and vagal nerve-dependent manner. Single-nucleus RNA-seq of the nTS at baseline and following allergen challenges reveals that a Dbh+ population is preferentially activated. Ablation or chemogenetic inactivation of Dbh+ nTS neurons blunted, while chemogenetic activation promoted hyperreactivity. Viral tracing indicates that Dbh+nTS neurons, capable of producing norepinephrine, project to the NA, and NA neurons are necessary and sufficient to relay allergen signals to postganglionic neurons that then directly drive airway constriction. Focusing on transmitters, delivery of norepinephrine antagonists to the NA blunted allergen-induced hyperreactivity. Together, these findings provide molecular, anatomical and functional definitions of key nodes of a canonical allergen response circuit. The knowledge opens the possibility of targeted neural modulation as an approach to control refractory allergen-induced airway constriction.

cell biology↗

bioRxiv2023

Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis

Chronic inflammation and tissue fibrosis are common stress responses that worsen organ function, yet the molecular mechanisms governing their crosstalk are poorly understood. In diseased organs, stress-induced changes in gene expression fuel maladaptive cell state transitions and pathological interaction between diverse cellular compartments. Although chronic fibroblast activation worsens dysfunction of lung, liver, kidney, and heart, and exacerbates many cancers, the stress-sensing mechanisms initiating the transcriptional activation of fibroblasts are not well understood. Here, we show that conditional deletion of the transcription co-activator Brd4 in Cx3cr1-positive myeloid cells ameliorates heart failure and is associated with a dramatic reduction in fibroblast activation. Analysis of single-cell chromatin accessibility and BRD4 occupancy in vivo in Cx3cr1-positive cells identified a large enhancer proximal to Interleukin-1 beta (Il1b), and a series of CRISPR deletions revealed the precise stress-dependent regulatory element that controlled expression of Il1b in disease. Secreted IL1B functioned non-cell autonomously to activate a p65/RELA-dependent enhancer near the transcription factor MEOX1, resulting in a profibrotic response in human cardiac fibroblasts. In vivo, antibody-mediated IL1B neutralization prevented stress-induced expression of MEOX1, inhibited fibroblast activation, and improved cardiac function in heart failure. The elucidation of BRD4-dependent crosstalk between a specific immune cell subset and fibroblasts through IL1B provides new therapeutic strategies for heart disease and other disorders of chronic inflammation and maladaptive tissue remodeling.

molecular biology↗

bioRxiv2022

Characterization of a novel botybirnavirus with a unique dsRNA infecting Didymella theifolia from tea plants

Didymella theifolia specifically infects some local varieties of Camellia sinensis in China, representing a unique fungal species, and characterization of the mycoviruses related to this fungal species is attractive. Three double-stranded RNAs (dsRNAs; dsRNAs 1, 2 and 3 with sizes of 6338, 5910 and 727 bp, respectively) were identified in an avirulent strain CJP4-1 of D. theifolia exhibiting normal growth and morphologies. Characterization of the dsRNAs 1 and 2 revealed that they are genomic components of a novel botybirnavirus, tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1), and encapsidated in isometric virions with a size of [~]39.8 nm in diameter. It is worth noting that dsRNA3 shares no detectable identity with those sequences deposited in NCBI database, while a high identity (36.58% and 40.93%) with the left regions of dsRNAs 1 and 2, but is not encapsidated in DtBRV1 particles, suggesting it is a unique dsRNA unit that is not a DtBRV1 component or a satellite and its taxonomic classification remains unclear. SDS-polyacrylamide gel electrophoresis in combination with peptide mass fingerprint analysis revealed that DtBRV1 capsid protein consisting of polypeptides encoded by the left regions of both genomic components. DtBRV1 is efficiently vertically transmitted through conidia while difficult in horizontal transmission from strain CJP4-1 to other strains. DtBRV1 has no effects on fungal growth and virulence as accessed with the transfectants of virulent strain JYC1-6 of D. theifolia infected by DtBRV1. DtBRV1 with specific molecular traits contributes useful information for a better understanding of the mycoviral community. ImportanceTea plants represent an ancient and unique plant species community cultured in China, while the mycoviruses related to the phytopathogenetic fungi infecting tea remain limited. Here, we characterized a novel botybirnavirus (tentatively named Didymella theifolia botybirnavirus1 (DtBRV1), and a specific dsRNA infecting Didymella theifolia responsible for a noticeable disease of tea plants. DtBRV1 contains two dsRNAs (1 and 2) encapsidated in isometric virions in size of [~]39.8 nm, while dsRNA3 is not encapsidated in the viral particles although it has a high identity with the mycoviral genomic components. Additionally, DtBRV1 coat proteins are composed of fused proteins encoded by both dsRNA-coding open reading frames most likely after cleave and fuse processing progress, which is striking unlike most mycoviruses. With some specific molecular traits, DtBRV1 and the related specific dsRNA unit expand our understanding of virus diversity, taxonomy, and evolution.

microbiology↗

bioRxiv2022

A novel antidepressant acting via allosteric inhibition of GluN2D-incorporated NMDA receptors at GABAergic interneurons

N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated calcium-permeable excitatory channels. They have attracted great interest as potential targets for the treatment of depression in recent years. NMDARs typically assemble as heterotetramers composed of two GluN1 and two alternative GluN2 (2A-2D) subunits, the latter of which endow various subtypes with diverse gating and pharmacological properties. To date, limited molecules with GluN2 specificity have been identified to show antidepressant effects. Here, we identify a compound termed YY-23 extracted from Rhizoma Anemarrhenae allosterically inhibited the channel activities of GluN2C- or GluN2D-incorporated NMDARs, an effect that was presumably influenced by the S2 segment in the ligand-binding domain of the GluN2 subunit. We found that prefrontal GluN2D-containing NMDARs were predominantly expressed at GABAergic interneurons rather than pyramidal neurons. Furthermore, we revealed that YY-23 suppressed the activity of GluN2D-containing NMDARs and GABAergic neurotransmission in the medial prefrontal cortex (mPFC). As a consequence, this GABAergic disinhibition facilitated the excitatory transmission. Behavioural experiments showed that YY-23 acted as a rapid antidepressant in both stress-naive and stressed animal models, which was abolished in Grin2d-knockout mice. Together, our findings suggest that GluN2D-incorporated NMDARs on GABAergic interneurons might be promising therapeutic targets for the treatment of depression.

neuroscience↗

bioRxiv2022

Accurate de novo prediction of RNA 3D structure with transformer network

RNA 3D structure prediction remains challenging though after years of efforts. Inspired by the recent breakthrough in protein structure prediction, we developed trRosettaRNA, a novel deep learning-based approach to de novo prediction of RNA 3D structure. Like trRosetta, the trRosettaRNA pipeline comprises two major steps: 1D and 2D geometries prediction by a transformer network; and full-atom 3D structure folding by energy minimization with constraints from the predicted geometries. We benchmarked trRosettaRNA on two independent datasets. The results show that trRosettaRNA outperforms other conventional methods by a large margin. For example, on 25 targets from the RNA-Puzzles experiments, the mean RMSD of the models predicted by trRosettaRNA is 5.5 [A], compared with 10.5 [A] from the state-of-the-art human group (i.e., Das). Further comparisons with two recently released deep learning-based methods (i.e., DeepFoldRNA and RoseTTAFoldNA) show that all three methods have similar accuracy. However, trRosettaRNA yields more accurate and physically more realistic side-chain atoms than DeepFoldRNA and RoseTTAFoldNA. Finally, we apply trRosettaRNA to predict the structures for the Rfam families that do not have known structures. Analysis shows that for 263 families, the predicted structure models are estimated to be accurate with RMSD < 4 [A]. The trRosettaRNA server and the package are available at: https://yanglab.nankai.edu.cn/trRosettaRNA/.

bioinformatics↗

bioRxiv2022

Influence of MUC1 on trafficking of TRPV5 and TRPV6 and in vivo Ca2+ homeostasis.

Polymorphism of the gene encoding mucin 1 (MUC1) is associated with skeletal and dental phenotypes in human genomic studies. Animals lacking MUC1 exhibit mild reduction in bone density. These phenotypes could be a consequence of modulation of bodily Ca homeostasis by MUC1, as suggested by the previous observation that MUC1 enhances cell surface expression of the Ca2+-selective channel, TRPV5 in cultured unpolarized cells. Using biotinylation of cell-surface proteins, we asked whether MUC1 influences endocytosis of TRPV5 and another Ca2+-selective TRP channel, TRPV6, in cultured polarized epithelial cells. Results indicate that MUC1 reduces endocytosis of both channels, enhancing cell surface expression. Further, mice lacking MUC1 lose apical localization of TRPV5 and TRPV6 in the renal tubular and duodenal epithelium. Females, but not males, lacking MUC1 exhibit reduced blood Ca2+. However, mice lacking MUC1 exhibited no differences in basal urinary Ca excretion or Ca retention in response to PTH receptor signaling, suggesting compensation by transport mechanisms independent of TRPV5 and TRPV6. Finally, humans with autosomal dominant tubulointerstitial kidney disease due to frame-shift mutation of MUC1 (ADTKD-MUC1) exhibit reduced plasma Ca concentrations compared to control individuals with mutations in the gene encoding uromodulin (ADTKD-UMOD), consistent with MUC1 haploinsufficiency causing reduced bodily Ca2+.

physiology↗

bioRxiv2022

Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat

The success of common wheat as the global staple crop is derived from genome diversity and redundancy as a result of allopolyploidization [1-3], giving rise to the major question how the divergent and convergent transcription among different subgenomes are achieved and harmonized in a single cell. The regulatory information is largely encoded in DNA regulatory elements (REs) interpreted by sequence specific transcription factors (TFs). Here, we created a catalog of genome-wide TF-binding sites (TFBS) to assemble an extensive wheat regulatory network comprising connections among 189 TFs and 3,714,431 REs, which enhances the understanding of wheat regulatory mechanisms on an unprecedented scale. A significant fraction of subgenome-divergent TFBS are derived from recent subgenome-asymmetric expansion of particular transposable element (TE) families. In contrary, TFBS derived from ancient TE expansion largely underwent parallel purifying selection during independent evolution of each subgenome, despite extensive unbalanced turnover of flanking TEs. Altogether, the subgenome-convergent and -divergent regulation in common wheat is orchestrated via differential evolutionary selection on paleo- and neo-TEs.

bioinformatics↗

bioRxiv2022

HY5 Regulates GLK and GNC Transcription Factors to Orchestrate Photomorphogenesis in Arabidopsis thaliana

Light induced de-etiolation is an important aspect of seedling photomorphogenesis. GOLDEN2 LIKE (GLK) transcriptional regulators are involved in chloroplast development, but to what extent they participate in photomorphogenesis is not clear. Here we show that ELONGATED HYPOCOTYL5 (HY5) binds to GLK promoters to activate their expression, and also interacts with GLK proteins. Chlorophyll content in the de-etiolating Arabidopsis seedlings of the hy5 glk2 double mutants was lower than that in hy5 single mutant. GLKs inhibited hypocotyl elongation, and the phenotype could superimpose on the hy5 phenotype. Correspondingly, GLK2 regulates the expression of photosynthesis and cell elongation genes partially independent of HY5. Before exposed to light, the accumulation of GLK proteins was regulated by DE-ETIOLATED 1 (DET1), while also affected (especially for GLK1) transcriptionally by HY5. The enhanced etioplast development and photosystem gene expression observed in det1 mutant were attenuated in det1 glk2 double mutant. Our study reveals that GLKs act down-stream of HY5 and likely cooperate with HY5 and DET1, to orchestrate multiple developmental traits during the light-induced skotomorphogenesis to photomorphogenesis transition in Arabidopsis. One-sentence summaryGLK and GNC act downstream of HY5, and cooperate with HY5 and DET1, to regulate both chloroplast development and hypocotyl elongation during the transition from skotomorphogenesis to photomorphogenesis.

plant biology↗

bioRxiv2022

CURLYLEAF is a key modulator of apoplast water status in Arabidopsis leaf

The apoplast of plant leaf, the intercellular space between mesophyll cells, is normally largely filled with air with a minimal amount of water in it, which is essential for key physiological processes such as gas exchange to occur. Interestingly, phytopathogens exploit virulence factors to induce a water-rich environment, known as "water soaking", in the apoplast of the infected leaf tissue to promote disease. We propose that plants evolved a "water soaking" pathway, which normally keeps a "minimized and balanced" water level in the leaf apoplast for plant growth but is disturbed by microbial pathogens to facilitate infection. Investigation of the "water soaking" pathway and leaf water control mechanisms is a fundamental, yet previously-overlooked, aspect of plant physiology. To identify key components in the "water soaking" pathway, we performed a genetic screen to isolate Arabidopsis severe water soaking (sws) mutants that show leaf water over-accumulation under high air humidity, a condition required for visible water soaking. Here we report the sws1 mutant, which displays rapid water soaking upon high humidity treatment due to a loss-of-function mutation in CURLY LEAF (CLF), encoding a histone methyl-transferase in the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2). We found that the sws1 (clf) mutant exhibits an enhanced abscisic acid (ABA) level and stomatal closure, which are indispensable for its water soaking phenotype and mediated by CLFs direct regulation of a group of ABA-associated NAC transcription factors, NAC019/055/072. Interestingly, the clf mutant showed a weakened immunity, which likely also contributes to the water soaking phenotype. In addition, the clf plant supports a significantly higher level of Pseudomonas syringae pathogen-induced water soaking and bacterial multiplication, in an ABA pathway and NAC019/055/072-dependent manner. Collectively, our study probes into a fundamental question in plant biology and demonstrates CLF as a key modulator of leaf water status via epigenetic regulation of ABA pathway and stomatal movement.

plant biology↗

bioRxiv2022

Single Cell Epigenetics Reveal Cell-Cell Communication Networks in Normal and Abnormal Cardiac Morphogenesis

Communication between myriad cell types during organ formation underlies proper morphogenesis1. In cardiac development, reciprocal signaling between mesoderm progenitors and neural crest cells is essential, and its disruption leads to congenital heart malformations, the most common human birth defect. However, mechanistic interrogation of temporal gene networks and cis regulatory elements in this crosstalk is limited2,3. Here, we integrated single cell chromatin accessibility and transcriptomics to establish an unbiased and temporal epigenomic map of the embryonic mouse heart over multiple stages and developed machine learning models to predict enhancers for heart and neural crest. We leveraged these advances to determine the consequences of dysregulated signaling at single cell resolution caused by deletion of TBX1, a transcription factor that causes morphogenetic defects of the cardiac outflow tract in humans and functions non-cell autonomously in cardiac mesodermal progenitors to direct pharyngeal neural crest differentiation4-6. Loss of Tbx1 in mice led to broad closure of chromatin regions enriched in cardiac progenitor transcription factor motifs within a narrow subset of cardiac mesodermal progenitors and correlated with diminished expression of numerous members of the fibroblast growth factor, retinoic acid, Notch and Semaphorin pathways. In affected progenitors, ectopic accessibility and expression of posterior heart field factors in the anterior heart field suggested impaired axial patterning. In response, a subset of cardiac neural crest cells displayed epigenomic and transcriptional defects, indicating a failure of differentiation corresponding to dysregulation of the anterior-posterior gradient of pharyngeal Hox gene expression. This study demonstrates that single-cell genomics and machine learning can generate a mechanistic model for how disruptions in cell communication selectively affect spatiotemporally dynamic regulatory networks in cardiogenesis.

developmental biology↗

bioRxiv2022

Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes

Birth defects occur in [~]6% of all live births and can be caused by combinations of genetic and environmental influences1. Large-scale DNA sequencing efforts are revealing genetic influences2,3, but investigations into the contributions of environmental factors have largely been limited to association studies with limited mechanistic insight. Hyperglycemia present in pre-gestational diabetic mothers is among the most frequent environmental contributor to congenital defects and results in an increased incidence of congenital heart defects and craniofacial anomalies4. However, the cell types involved and underlying mechanisms by which maternal hyperglycemia affects these regions are unknown. Here, we utilized multi-modal single cell analyses to reveal that maternal diabetes affects the epigenomic and transcriptomic state of specific subsets of cardiac and craniofacial progenitors during embryogenesis. A previously unrecognized subpopulation of anterior heart field progenitors expressing Alx3 acquired a more posterior identity in response to maternal hyperglycemia, based on gene expression and chromatin status. Similarly, a sub-population of neural crest-derived cells in the second pharyngeal arch, which contributes to craniofacial structures, also displayed abnormalities in cell specification and patterning. Analysis of differentially accessible chromatin regions demonstrated that disrupted patterning was associated with increased intrinsic retinoic acid signaling in affected cell types in response to maternal diabetes and hyperglycemia. This work demonstrates how an environmental insult can have highly selective epigenomic consequences on discrete cell types leading to developmental patterning defects.

developmental biology↗

bioRxiv2022

Gibberellins promote polar auxin transport to regulate stem cell fate decisions in cambium

Vascular cambium contains bifacial stem cells, which produce secondary xylem to one side and secondary phloem to the other. However, how these fate decisions are regulated is unknown. Here, we show that the positioning of an auxin signalling maximum within the cambium determines the fate of stem cell daughters. The position is modulated by gibberellin-regulated, PIN1-dependent polar auxin transport. Gibberellin treatment broadens auxin maximum from the xylem side of the cambium towards the phloem. As a result, xylem-side stem cell daughter preferentially differentiates into xylem, while phloem-side daughter retains stem cell identity. Occasionally, this broadening leads to direct specification of both daughters as xylem, and consequently, adjacent phloem-identity cell reverts to being stem cell. Conversely, reduced gibberellin levels favour specification of phloem-side stem cell daughter as phloem. Together, our data provide a mechanism by which gibberellin regulates the ratio of xylem and phloem production.

plant biology↗

bioRxiv2022

Talaromyces marneffei suppresses human macrophages inflammatory by producing the truncated protein NCOR2-013 via TUT1-regulated alternative splicing

Talaromyces marneffei (T. marneffei) immune-escaping is an important factor for high mortality of talaromycosis. It is currently known that T. marneffei performs these functions through a variety of strategies, however, the role of alternative splicing (AS) in this process is poorly understood. Here we depicted the AS landscape in the macrophage upon T. marneffei infection via high-throughput RNA sequencing. Moreover, we identified a truncated protein of NCOR2/SMRT, namedly NCOR2-013, was significantly upregulated upon T. marneffei infection. Mechanistic analysis indicates that NCOR2-013 forms a co-repression complex with TBL1XR1/TBLR1 and HDAC3, thereby inhibiting JunB-mediated transcriptional activation of pro-inflammatory cytokines via the inhibition of histone acetylation. Also, we identified TUT1 as the AS regulator that involved in facilitating T. marneffei immune evasion via regulation of NCOR2-013 production. Collectively, the findings indicate that T. marneffei escapes macrophages killing through the TUT1-mediated the alternative splicing of NCOR2-013, which providing a new insight into the molecular mechanisms of T. marneffei immune evasion, and a potential targets for talaromycosis therapy.

microbiology↗

bioRxiv2022

Impaired neuromodulator crosstalk delays vigilance-dependent astroglia Ca2+ activation in mouse models of Alzheimer's disease

Degeneration in neuronal nuclei producing the neuromodulators acetylcholine and norepinephrine is a hallmark of Alzheimers disease (AD). Therapeutic interventions that increase acetylcholine in brain ameliorate AD symptoms in human patients, and augmenting norepinephrine restores cognitive function in mouse models of AD as well as Down Syndrome, the most frequent cause of early onset AD. A prominent cellular target of noradrenergic and potentially cholinergic signaling during states of heightened vigilance are astroglia and recent studies indicate that astroglia Ca2+ dynamics in awake mice contribute to optimal cognitive performance. Here we tested the hypothesis that vigilance-dependent Ca2+ signaling in mouse primary visual cortex astrocytes is altered in mouse models of AD and provide mechanistic insight into upstream neuromodulator signaling that shapes astrocyte Ca2+ dynamics in healthy and AD conditions. In two mouse models of AD (APPswe/PSEN1dE9 and AppNL-F KI), we consistently observed delayed and less coordinated astrocyte Ca2+ elevations in response to locomotion, a well-controlled behavioral paradigm triggering widespread Ca2+ activation in astroglia throughout the brain. Combining pharmacological and genetic manipulations, we found that noradrenergic signaling to astrocytes was facilitated by cholinergic signaling, but this neuromodulator crosstalk was impaired in AppNL-F mice. Pharmacological facilitation of norepinephrine release rescued delayed and less coordinated astrocyte Ca2+ activation in AppNL-F mice and suggests that astrocytes preserve a functional reserve that can be recruited even during late-stage disease. Our findings of delayed and less coordinated astroglia Ca2+ activation predict impaired noradrenergic signaling and may contribute to the cognitive decline in AD.

neuroscience↗

bioRxiv2022

Constraints of vigilance-dependent noradrenergic signaling to mouse cerebellar Bergmann glia

Behavioral state plays an important role in determining astroglia Ca2+ signaling. In particular, locomotion-mediated elevated vigilance has been found to trigger norepinephrine-dependent whole cell Ca2+ elevations in astroglia throughout the brain. For cerebellar Bergmann glia it has recently been found that locomotion-induced transient Ca2+ elevations depend on their 1A-adrenergic receptors. With increasing availability and implementation of locomotion as behavioral parameter it becomes important to understand the constraints of noradrenergic signaling to astroglia. Here we evaluated the effect of speed, duration and interval of locomotion on Ca2+ signals in Bergmann glia as well as cerebellar noradrenergic axon terminals. We found almost no dependence on locomotion speed, but following the initial Ca2+ transient prolonged locomotion events revealed a steady-state Ca2+ elevation. Comparison of time course and recovery of transient Bergmann glia and noradrenergic terminal Ca2+ dynamics suggested that noradrenergic terminal Ca2+ activity determines Bergmann glia Ca2+ activation and does not require noradrenergic receptor desensitization to account for attenuation during prolonged locomotion. Further, analyzing the correlation among Ca2+ dynamics within regions within the field of observation we found that coordinated activity among noradrenergic terminals accounts for fluctuations of steady-state Bergmann glia Ca2+ activity. Together, our findings will help to better understand astroglia Ca2+ dynamics during less controlled awake behavior and may guide the identification of behavioral contexts preferably dependent on astroglia Ca2+ signaling.

neuroscience↗

bioRxiv2022

Single-Cell RNA-Seq Uncovers Dynamic Processes Orchestrated by RNA-Binding Protein DDX43 in Chromatin Remodeling during Spermiogenesis

Advances in single-cell RNA sequencing (scRNA-seq) have allowed for elucidating biological mechanisms at cell state level. Mammalian spermatogenic process showcases dynamic switches of gene expression pattern with delicate morphological and functional alterations of germ cells, but it is unclear how such dynamics is genetically controlled. Here we demonstrate that mouse testis-enriched RNA helicase DDX43, as well as its ATP hydrolysis site, is required for spermiogenesis. Genetic mutation of Ddx43 renders spermatids heterogeneously defective in multiple steps of chromatin remodeling, resulting in incomplete substitution of transition protein by protamine and less condensed sperm nucleus. Through scRNA-seq analyses of testicular cells derived from adult wild-type and Ddx43 mutant testes in mice, we reveal that the DDX43 deficiency-elicited perturbation in the dynamic RNA regulatory processes underlies the differentiation deficiency of spermatids. Further, focused analyses on early-stage spermatids combined with enhanced CLIP sequencing (eCLIP-seq) identify Elfn2 as DDX43-targeted hub gene, whose in vivo knockdown shows similar phenotypic defects as Ddx43 mutant. Our study illustrates an essential role for DDX43 in post-meiotic chromatin remodeling and highlights the single cell-based strategy for a refined dissection of stage-specific regulation of germline differentiation.

developmental biology↗