Biology subjects

Ge, W.

Publications and source records attributed to Ge, W..

47 records · Page 3Linked to original sources

bioRxiv2020

Differentiation genes were governed by DNA methylation during hair follicle morphogenesis in Cashmere goat

DNA methylation plays a critical role in early embryonic skin development by controlling gene expression. Act as an indirect regulator, long non-coding RNA (lncRNA) recruit DNA methyltransferases to specific genomic sites to methylate DNA. However, the molecular regulation mechanisms underlying hair follicle morphogenesis is unclear in cashmere goat. In this study, RNA-seq and Whole-genome bisulfite sequencing (WGBS) in embryonic day 65 (E65) and E120 skin tissues of cashmere goat were used to reveal this complex regulatory process. RNA-seq, qRT-PCR and immunohistochemistry results showed that Wnt signaling played an important role in both hair follicle induction and differentiation stage, transcriptional factors (TFs) including Hoxc13, Sox9, Sox21, Junb, Lhx2, Vdr and Gata3 participated in hair follicle differentiation via specific expression at E120. Subsequently, combination of WGBS and RNA-seq analysis showed that the expression of hair follicle differentiation genes and TFs genes was negatively correlated with DNA methylation level generally. A portion of hair follicle differentiation genes were methylated and repressed in hair follicle induction stage but were subsequently demethylated and expressed during hair follicle differentiation stage, suggesting DNA methylation play an important role in hair morphogenesis through regulating associated gene expression. Furthermore, the potential differentially expressed lncRNAs associated with DNA methylation on target gene were revealed. LncRNA XR_001918556 may affect the DNA methylation of TFs gene Gata3, lnc-003786 may affect the DNA methylation of signaling gene Fgfr2. In conclusion, differentiation genes were governed by DNA methylation, resulting in repressed expression in hair follicle induction stage and high expression in hair follicle differentiation stage. Furtherly, potential lncRNAs associated with DNA methylation on target genes were delineated. This study would enrich the regulatory network and molecular mechanisms on hair morphogenesis.

developmental biology↗

bioRxiv2019

Dissecting the initiation of female meiosis in the mouse at single-cell resolution

Germ cell meiosis is one of the most finely orchestrated events during gametogenesis with distinct developmental patterns in males and females. However, in mammals, the molecular mechanisms involved in this process remain not well known. Here, we report detailed transcriptome analyses of cell populations present in the mouse female gonadal ridges (E11.5) and the embryonic ovaries from E12.5 to E14.5 using single cell RNA sequencing (scRNA seq). These periods correspond with the initiation and progression of meiosis throughout the first stage of prophase I. We identified 13 transcriptionally distinct cell populations and 7 transcriptionally distinct germ cell subclusters that correspond to mitotic (3 clusters) and meiotic (4 clusters) germ cells. By comparing the signature gene expression pattern of 4 meiotic germ cell clusters, we found that the 4 cell clusters correspond to different cell status en route to meiosis progression, and therefore, our research here characterized detailed transcriptome dynamics during meiotic prophase I. Reconstructing the progression of meiosis along pseudotime, we identified several new genes and molecular pathways with potential critical roles in the mitosis/meiosis transition and early meiotic progression. Last, the heterogeneity within somatic cell populations was also discussed and different cellular states were identified. Our scRNA seq analysis here represents a new important resource for deciphering the molecular pathways driving meiosis initiation and progression in female germ cells and ovarian somatic cells.

developmental biology↗

bioRxiv2019

Transcriptome Landscape Reveals Underlying Mechanisms of Ovarian Cell Fate Differentiation and Primordial Follicle Assembly

Primordial follicle assembly in mammals occurs at perinatal ages and largely determines the ovarian reserve available to support the reproductive lifespan. The primordial follicle structure is generated by a complex network of interactions between oocytes and ovarian somatic cells that remain poorly understood. In the present research, using single-cell RNA sequencing performed over a time-series on mouse ovaries coupled with several bioinformatics analyses, the complete dynamic genetic programs of germ and granulosa cells from E16.5 to PD3 are reported for the first time. The time frame of analysis comprises the breakdown of germ cell cysts and the assembly of primordial follicles. Confirming the previously reported expression of genes by germ cells and granulosa cells, our analyses identified ten distinct gene clusters associated to germ cells and eight to granulosa cells. Consequently, several new genes expressed at significant levels at each investigated stage were assigned. Building single-cell pseudo temporal trajectories five states and two branch points of fate transition for the germ cells, and three states and one branch point for the granulosa cells were revealed. Moreover, GO and ClueGO term enrichment enabled identifying biological processes, molecular functions and cellular components more represented in germ cells and granulosa cells or common to both cell types at each specific stage. Finally, by SCENIC algorithm, we were able to establish a network of regulons that can be postulated as likely candidates for sustaining germ cell specific transcription programs throughout the investigated period.

developmental biology↗

bioRxiv2019

PulseDIA: in-depth data independent acquisition mass spectrometry using enhanced gas phase fractionation

An inherent bottleneck of data independent acquisition (DIA) analysis by Orbitrap-based mass spectrometers is the relatively large window width due to the relatively slow scanning rate compared to TOF. Here we present a novel gas phase separation and MS acquisition method called PulseDIA-MS, which improves the specificity and sensitivity of Orbitrap-based DIA analysis. This is achieved by dividing the ordinary DIA-MS analysis covering the entire mass range into multiple injections for DIA-MS analyses with complementary windows. Using standard HeLa digests, the PulseDIA method identified 69,530 peptide precursors from 9,337 protein groups with ten MS injections of 30 min LC gradient. The PulseDIA scheme containing two complementary windows led to the highest gain of peptide and protein identifications per time unit compared to the conventional 30 min DIA method. We further applied the method to profile the proteome of 18 cholangiocarcinoma (CCA) tissue samples (benign and malignant) from nine patients. PulseDIA identified 7,796 protein groups in these CCA samples, with 14% increase of protein identifications, compared to the conventional DIA method. The missing value for protein matrix dropped by 7% with PulseDIA acquisition. 681 proteins were significantly dysregulated in tumorous CCA samples. Together, we presented and benchmarked an alternative DIA method with higher sensitivity and lower missing rate.

cancer biology↗

bioRxiv2019

Single-cell transcriptome profiling reveals dermal and epithelium cell fate decisions during embryonic hair follicle development

Characterization of the morphological structure during hair follicle development has been well documented, while the current understanding of the molecular mechanisms involved in follicle development remain limited. Here, using unbiased single-cell RNA sequencing, we analyzed 15,086 single cell transcriptome profiles from E13.5 and E16.5 fetal mice, and newborn mouse (postnatal day 0, P0) dorsal skin cells. Based on t-distributed Stochastic Neighbor Embedding (tSNE) clustering, we identified 14 cell clusters from skin cells and delineated their cell identity gene expression profiles. Pseudotime ordering analysis successfully constructed epithelium/dermal cell lineage differentiation trajectory and revealed sequential activation of key regulons involved during cell fate decisions. Along with this, intercellular communication between different cell populations were inferred based on a priori knowledge of ligand-receptor pairs. Together, our findings here provide a molecular landscape during hair follicle epithelium/dermal cell lineage fate decisions, and more importantly, recapitulate sequential activation of core regulatory transcriptional factors for different cell populations during hair follicle morphogenesis.

developmental biology↗

bioRxiv2019

The lncRNAs Implicated in Redox Regulation in Ybx1 Deficient Zebrafish Larvae

Ybx1 has been demonstrated as a crucial gene in embryogenesis, reproduction as well as development in various vertebrates such as mouse and zebrafish. However, the underlying lncRNA-mediated mechanisms require deep investigation. Particularly, the importance of lncRNA to vertebrate development is controversial and questionable since many studies have yielded contradictory conclusions for the same lncRNAs. In the present study, in order to disclose the lncRNAs implicated in vertebrate development, a systematic transcriptome analysis is conducted based on the RNA sequencing data derived from ybx1 homozygous mutant zebrafish on day5 (day5_ybx1-/-) as well as wild type zebrafish on day5 and day6 (day5_ybx1+/+, day6_ybx1+/+). A high-confidence dataset of zebrafish lncRNAs is detected using a stepwise filtering pipeline. Differential expression analysis and co-expression network analysis reveal that several lncRNAs probably act on duox and noxo1a, the genes related to redox (reduction-oxidation reaction) processes which are triggered by ybx1 disruption. Validation by an experimental study on three selected lncRNAs indicates that knockdown of all selected lncRNAs leads to morphological deformation of larvae. In addition, our experiments effectively support the prediction of network analysis in many interaction patterns between the selected lncRNAs and the two redox genes (duox, noxo1a). In short, our study provides new insights into the function and mechanism of lncRNAs implicated in zebrafish embryonic development and demonstrates the importance of lncRNAs in vertebrate development.\n\nAuthor SummaryLncRNAs has been emerged as key regulatory layers because of their multiple functions in diverse biological processes and pathways. However, there is disagreement about the roles of lncRNAs in vertebrate development Some cases demonstrated that lncRNAs was important to development. Others showed that lncRNAs just have feeble functions in development. On the other hand, Ybx1 processing multi-functions has been well demonstrated as a key protein to most vertebrate in development. Hence, aimed at disclosure of key lncRNAs implicated in vertebrate development as well as their possible roles, we performed a systematic transcriptome analysis based on the deep RNA sequencing data of ybx1 homozygous mutant zebrafish and wild type zebrafish. Our analysis successfully revealed several lncRNAs probably target on the redox-related genes. Furthermore, our experiments validated the importance of these lncRNAs to zebrafish embryo development. This study is the first to utilize Ybx1 as breakpoint to identify key lncRNA related to vertebrate development and provides new insights into underlying mechanisms of lncRNAs in development.

developmental biology↗

bioRxiv2019

Systematic comparative analysis of single cell RNA-sequencing methods

A multitude of single-cell RNA sequencing methods have been developed in recent years, with dramatic advances in scale and power, and enabling major discoveries and large scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single cell and/or single nucleus profiling from three types of samples - cell lines, peripheral blood mononuclear cells and brain tissue - generating 36 libraries in six separate experiments in a single center. To analyze these datasets, we developed and applied scumi, a flexible computational pipeline that can be used for any scRNA-seq method. We evaluated the methods for both basic performance and for their ability to recover known biological information in the samples. Our study will help guide experiments with the methods in this study as well as serve as a benchmark for future studies and for computational algorithm development.

genomics↗

bioRxiv2019

Mitochondrial Ca2+ influences photoresponse recovery, metabolism, and mitochondrial localization in cone photoreceptors

Mitochondrial Ca2+ regulates key cellular processes including cytosolic Ca2+ signals, energy production, and susceptibility to apoptosis. Photoreceptors are specialized neurons that have extraordinarily high energy demands and rely on cytosolic Ca2+ signals for light adaptation and neurotransmission. Here we show that unlike other neurons zebrafish cone photoreceptors express low levels of the mitochondrial Ca2+ uniporter (MCU), the channel that allows mitochondrial Ca2+ entry. To determine why MCU expression is kept low, we overexpressed MCU specifically in cones. This increases mitochondrial [Ca2+], causes faster cytosolic Ca2+ clearance, and accelerates photoresponse recovery. Moreover, flux through the citric acid cycle increases despite dramatic changes in mitochondrial ultrastructure and localization. Remarkably, cones survive this ongoing stress until late adulthood. Our findings demonstrate the importance of tuning mitochondrial Ca2+ influx to modulate physiological and metabolic processes and reveal a novel directed movement of abnormal mitochondria in photoreceptors.

cell biology↗

bioRxiv2018

Systems Biology Understanding of the Effects of Lithium on Cancer.

Lithium has many widely varying biochemical and phenomenological effects, suggesting that a systems biology approach is required to understand its action. Multiple lines of evidence point to lithium as a significant factor in development of cancer, showing that understanding lithium action is of high importance. In this paper we undertake first steps towards a systems approach by analyzing mutual enrichment between the interactomes of lithium-sensitive enzymes and the pathways associated with cancer. This work integrates information from two important databases, STRING and KEGG pathways. We find that for the majority of cancer pathways the mutual enrichment is many times greater than chance, reinforcing previous lines of evidence that lithium is an important influence on cancer.

cancer biology↗

bioRxiv2018

PRL-1 is required for neuroprotection against olfactory CO2 stimulation in Drosophila

The Mammalian phosphatase of regenerating liver (PRL) family is primarily recognized for its oncogenic properties. Here we found that in Drosophila, loss of prl-1 resulted in CO2-induced brain disorder presented as irreversible wing hold up with enhancement of Ca2+ responses at the neuron synaptic terminals. Overexpression of Prl-1 in the nervous system could rescue the mutant phenotype. We show that Prl-1 is particularly expressed in CO2-responsive neural circuit and the higher brain centers. Ablation of the CO2 olfactory receptor, Gr21a, suppressed the mutant phenotype, suggesting that CO2 acts as a neuropathological substrate in absence of Prl-1. Further studies found that the wing hold up is an obvious consequence upon knockdown of Uex, a magnesium transporter, which directly interacts with Prl-1. Conditional expression of Uex in the nervous system could rescue the phenotype of prl-1 mutants. We demonstrate that Uex acts genetically downstream of Prl-1. Our findings provide important insights into mechanisms of Prl-1 protection against olfactory CO2 stimulation induced brain disorder at the level of detailed neural circuits and functional molecular connections.

neuroscience↗

bioRxiv2017

Using Optimal F-Measure and Random Resampling in Gene Ontology Enrichment Calculations

BackgroundA central question in bioinformatics is how to minimize arbitrariness and bias in analysis of patterns of enrichment in data. A prime example of such a question is enrichment of gene ontology (GO) classes in lists of genes. Our paper deals with two issues within this larger question. One is how to calculate the false discovery rate (FDR) within a set of apparently enriched ontologies, and the second how to set that FDR within the context of assessing significance for addressing biological questions, to answer these questions we compare a random resampling method with a commonly used method for assessing FDR, the Benjamini-Hochberg (BH) method. We further develop a heuristic method for evaluating Type II (false negative) errors to enable utilization of F-Measure binary classification theory for distinguishing \"significant\" from \"non-significant\" degrees of enrichment.\n\nResultsThe results show the preferability and feasibility of random resampling assessment of FDR over the analytical methods with which we compare it. They also show that the reasonableness of any arbitrary threshold depends strongly on the structure of the dataset being tested, suggesting that the less arbitrary method of F-measure optimization to determine significance threshold is preferable.\n\nConclusionTherefore, we suggest using F-measure optimization instead of placing an arbitrary threshold to evaluate the significance of Gene Ontology Enrichment results, and using resampling to replace analytical methods

bioinformatics↗