Biology subjects

Huang, S.

Publications and source records attributed to Huang, S..

At least 415 records · Page 23Linked to original sources

bioRxiv2019

Enrichment in conservative amino acid changes among fixed and standing missense variations in slow evolving proteins

Proteins were first used in the early 1960s to discover the molecular clock dating method and remain in common usage today in phylogenetic inferences based on neutral variations. To avoid substitution saturation, it is necessary to use slow evolving genes. However, it remains unclear whether fixed and standing missense changes in such genes may qualify as neutral. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Macaca monkey, we found that the fraction of conservative amino acid mismatches between species was significantly higher in slow evolving proteins. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 genomes project data and found that missense SNPs in slow evolving proteins also had higher fraction of conservative changes, especially for common SNPs, consistent with more natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variations in slow evolving proteins are more likely to be neutral and hence better qualified for use in phylogenetic inferences.

evolutionary biology↗

bioRxiv2019

High-throughput isolation and culture of human gut bacteria with droplet microfluidics

Isolation and culture of gut bacteria enable testing for microbial roles in disease and may also lead to novel therapeutics. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for isolating and assaying microbiota members in picoliter droplets (MicDrop). MicDrop can be used to create millions of distinct bacterial colonies in a single experiment while using off-the-shelf parts compact enough to fit in an anaerobic chamber. In proof-of-concept experiments, we used the platform to characterize inter-individual metabolic variation among hundreds of polysaccharide-degrading gut bacteria from nine stool donors. We also used MicDrop to test the hypothesis that growth kinetics of individual gut bacterial taxa are associated with longterm community dynamics in an artificial gut. These demonstrations suggest the MicDrop platform could support future diagnostic efforts to personalize microbiota-directed therapies, as well as to provide comprehensive new insights into the ecology of human gut microbiota.

microbiology↗

bioRxiv2019

Intraspecific diversity of fission yeast mitochondrial genome

The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 non-identical sequence types ranging from 17618 bp to 26910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analysing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the datasets generated in this study will facilitate future research on genome evolution.

evolutionary biology↗

bioRxiv2019

STXBP5/tomosyn regulates both the small Rho GTPase and the surface expression of AMPA receptors to control the dendritic stability of neurons

Tomosyn, a protein encoded by syntaxin-1-binding protein 5 (STXBP5) gene, has a well-established presynaptic role in the inhibition of neurotransmitter release and the reduction of synaptic transmission by its conical interaction with the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) machinery. The postsynaptic role of tomosyn in dendritic arborization, spine stability, and trafficking of ionotropic glutamate receptors remains to be elucidated. We used short hairpin RNA (shRNA) to knock down tomosyn in mouse primary neurons to evaluate the postsynaptic cellular function and molecular signaling regulated by tomosyn. Knockdown of tomosyn led to an increase of RhoA GTPase activity accompanied by compromised dendritic arborization, loss of dendritic spines, decreased surface expression of AMPA receptors, and reduced miniature excitatory postsynaptic current (mEPSC) frequency. Inhibiting RhoA signaling was sufficient to rescue the abnormal dendritic morphology and the surface expression of AMPA receptors. The function of tomosyn regulating RhoA is mediated through the N-terminal WD40 motif, where two variants each carrying a single nucleotide mutation in this region, were found in individuals with autism spectrum disorder (ASD). We demonstrated that these variants displayed loss-of-function phenotypes. Unlike the wild-type tomosyn, these two variants failed to restore the reduced dendritic complexity, spine density, as well as decreased surface expression of AMPA receptors in tomosyn knockdown neurons. This study uncovers a critical role of tomosyn, independent of its interaction with the SNARE machinery, in maintaining neuronal function by inhibiting RhoA activity. Further analysis of tomosyn variants also provides a potential mechanism for explaining cellular pathology in ASD.\n\nSignificance StatementThis study unveils a vital role of tomosyn in the maintenance of neuronal morphology, basal synaptic transmission, and AMPA receptor surface expression that is distinct from its presynaptic role. Tomosyn affects dendritic stability and glutamate receptor trafficking via the regulation of the Rho signaling pathway and this interaction is likely independent of the interaction with the dendritic SNARE complex, such as syntaxin-4. The WD40 domain of tomosyn is necessary to conduct the Rho regulation and two autism-associated variants localized at the WD40 domain perturb this function. The current study reveals a novel molecular link between dendritic stability and synaptic function, which could advance a greater understanding of the cellular pathologies involved in neurodevelopmental disorders, such as ASD.

neuroscience↗

bioRxiv2019

Human Chrysomya bezziana myiasis: A systematic review

BackgroundMyiasis due to Old World screw-worm fly, Chrysomya bezziana, is an important obligate zoonotic disease in the OIE-list of diseases and is found throughout much of Africa, the Indian subcontinent, southeast and east Asia. C. bezziana myiases cause not only morbidity and death to animals and humans, but also economic losses in the livestock industries. Because of the aggressive and destructive nature of this disease in hosts, we initiated this study to provide a comprehensive understanding of human myiasis caused by C. bezziana.\n\nMethodsWe conducted a systematic search of the databases in English (PubMed, Embase and African Index Medicus) and Chinese (CNKI, Wanfang, and Duxiu), and international government online reports to 6th February, 2019, to identify studies concerning Chrysomya bezziana. Another ten human cases in China and Papua New Guinea that our team had recorded were also included.\n\nResultsWe retrieved 1,048 reports from which 202 studies were ultimately eligible for inclusion in the present descriptive analyses. Since the first human case due to C. bezziana was reported in 1909, we have summarized 291 cases and found that these cases often occurred in poor hygiene, low socio-economic conditions, old age, and underlying diseases including infections, age-related diseases, and noninfectious chronic diseases. But C. bezziana myiasis appears largely neglected as a serious medical or veterinary condition, with human and animal cases only reported in 16 and 24 countries respectively, despite this fly species recorded as present in 44 countries worldwide.\n\nConclusionOur findings indicate that cryptic myiasis cases due to the obligate parasite, C. bezziana, are under-recognized. Through this in-depth study to clarify the knowledge of human C. bezziana myiasis including its etiology, clinical features, diagnosis, treatment, epidemiology, prevention and control, we call for more vigilance and awareness of the disease from governments, health authorities, clinicians, veterinary workers, nursing homes, and also the general public.\n\nAuthor summaryChrysomya bezziana larvae are characterized by feeding aggressively on the living tissues and body fluids of the host. The nightmare-like feelings of patients suffering from this myiasis, severe tissues and bones destruction, even death, and enormous economic loss in the livestock industries have been described in the previous reports. But our findings indicate that C. bezziana myiases still appear to be under-recognized as a serious medical or veterinary condition throughout the world. Both in China and the world at large, it is probable that C. bezziana distribution could be greater than currently reported. For the first time, we have therefore systematically investigated human myiasis caused by C. bezziana. Our study provides an opportunity for clinicians and health authorities to gain a better understanding of this disease from its etiology, pathology, clinical features, diagnosis, treatment, epidemiology, prevention and control. In addition, our findings will hopefully engage governments, health staff, veterinary workers, the elderly homes, and also the general public in efforts to recognize, prevent and control such infestations.

epidemiology↗

bioRxiv2019

Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect

Models of cancer cell population expansion assume exponential growth kinetics at low cell densities, with deviations from exponential growth only at higher densities due to limited resources such as space and nutrients. However, recent pre-clinical and clinical observations of tumor initiation or recurrence indicate the presence of tumor growth kinetics in which growth rates scale with cell numbers. These observations are analogous to the cooperative behavior of species in an ecosystem described by the ecological principle of the Allee effect. In preclinical and clinical models however, tumor growth data is limited by the lower limit of detection (i.e. a measurable lesion) and confounding variables, such as tumor microenvironment and immune responses may cause and mask deviations from exponential growth models. In this work, we present alternative growth models to investigate the presence of an Allee effect in cancer cells seeded at low cell densities in a controlled in vitro setting. We propose a stochastic modeling framework to consider the small number of cells in this low-density regime and use the moment approach for stochastic parameter estimation to calibrate the stochastic growth trajectories. We validate the framework on simulated data and apply this approach to longitudinal cell proliferation data of BT-474 luminal B breast cancer cells. We find that cell population growth kinetics are best described by a model structure that considers the Allee effect, in that the birth rate of tumor cells depends on cell number. This indicates a potentially critical role of cooperative behavior among tumor cells at low cell densities with relevance to early stage growth patterns of emerging tumors and relapse.\n\nAuthor SummaryThe growth kinetics of cancer cells at very low cell densities are of utmost clinical importance as the ability of a small number of newly transformed or surviving cells to grow exponentially and thus, to \"take off\" underlies tumor formation and relapse after treatment. Mathematical models of stochastic tumor cell growth typically assume a stochastic birth-death process of cells impacted by limited nutrients and space when cells reach high density, resulting in the widely accepted logistic growth model. Here we present an in-depth investigation of alternate growth models adopted from ecology to describe potential deviations from a simple cell autonomous birth-death model at low cell densities. We show that our stochastic modeling framework is robust and can be used to identify the underlying structure of stochastic growth trajectories from both simulated and experimental data taken from a controlled in vitro setting in which we can capture data from the relevant low cell density regime. This work suggests that the assumption of cell autonomous proliferation via a constant exponential growth rate at low cell densities may not be appropriate for all cancer cell growth dynamics. Consideration of cooperative behavior amongst tumor cells in this regime is critical for elucidating strategies for controlling tumor cell growth.

cancer biology↗

bioRxiv2019

Chemokine signaling links cell cycle progression and cilia formation for left-right symmetry breaking

Zebrafish dorsal forerunner cells (DFCs) undergo vigorous proliferation during epiboly and then exit cell cycle to generate Kupffers vesicle (KV), a ciliated organ necessary for establishing left-right (L-R) asymmetry. DFC proliferation defects are often accompanied by impaired cilia elongation in KV, but the functional and molecular interaction between cell-cycle progression and cilia formation remains unknown. Here we show that chemokine receptor Cxcr4a is required for L-R laterality by controlling DFC proliferation and KV ciliogenesis. Functional analysis revealed that Cxcr4a accelerates G1/S transition in DFCs and stabilizes Foxj1a, a master regulator of motile cilia, by stimulating Cyclin D1 expression through ERK1/2 signaling. Mechanistically, Cyclin D1-CDK4/6 drives G1/S transition during DFC proliferation and phosphorylates Foxj1a, thereby disrupting its association with Psmd4b, a 19S regulatory subunit. This prevents the ubiquitin-independent proteasomal degradation of Foxj1a. Our study uncovers a role for Cxcr4 signaling in L-R patterning and provides fundamental insights into the molecular linkage between cell-cycle progression and ciliogenesis.\n\nAuthor summaryDuring the organogenesis of zebrafish L-R organizer named KV, DFCs proliferate rapidly during epiboly and then exit the cell cycle to differentiate into ciliated epithelial KV cells. Cell cycle defects in DFCs are often accompanied by an alteration in KV cilia elongation. However, whether the cell cycle and cilia formation are mechanistically linked remains as an open question. In this study, we report that Cxcr4 signaling is required for DFC proliferation and KV ciliogenesis. We reveal that Cxcl12b/Cxcr4a signaling activates ERK1/2, which then promotes Cyclin D1 expression. Cyclin D1-CDK4/6 accelerates the G1/S transition in DFCs, while also facilitates cilia formation via stabilization of Foxj1a. Notably, Foxj1 undergoes proteasomal degradation via Ub-independent pathway during KV organogenesis. Our study further demonstrates that CDK4 phosphorylates and stabilizes Foxj1a by disrupting its association with Psmd4b, a 19S regulatory subunit. In summary, Cxcl12b/Cxcr4a chemokine signaling links cell cycle progression and cilia formation for L-R symmetry breaking via regulating Cyclin D1 expression.

developmental biology↗

bioRxiv2019

Modeling non-genetic dynamics of cancer cell states measured by single-cell analysis: Uncovering bifurcations that explain why treatment either kills a cancer cell or makes it resistant

Single-cell transcriptomics offers a new vista on non-genetic tumor cell plasticity, a neglected aspect of cancer. The gene expression state of each cell is governed by the gene regulatory network which represents a high-dimensional non-linear dynamical system that generates multiple stable attractor states and undergoes destabilizing bifurcations, manifest as critical transitions. Modeling clonal cell population as statistical ensembles of the same dynamical system, a index IC is derived for detecting destabilization towards critical transitions in single-cell molecular profiles. Therapy-induced bifurcation explains why treatment backfires: a drug-treated cell is imposed the binary choice to either apoptose or become a cancer-stem cell.

cancer biology↗

bioRxiv2019

Manure substitution of chemical fertilizer affect soil microbial community diversity, structure and function in greenhouse vegetable production systems

Soil microbial community and enzyme activities together affect various ecosystem functions of soils. Fertilization, as important agricultural management practices, are known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research therefore was to make a comparative study of the effects of different fertilization patterns (No N inputs (No N), 100% chemical fertilizer-N (CN) inputs (4/4CN) and different substitution rates of CN by organic manure-N (MN) (3/4CN+1/4MN, 2/4CN+2/4MN and 1/4CN+3/4MN)) on soil physicochemical properties, enzyme activities and microbial attributes in a GVP of Tianjin, China. Manure substitution of chemical fertilizer, especially at higher substitution rate (2/4CN+2/4MN and 1/4CN+3/4MN), improved soil physicochemical properties (higher soil organic C (SOC) and nutrient contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure addition caused a remarkable increase of the fungi/bacteria ratio and a distinct shift in the fungal (bacterial) community to greater abundance of arbuscular mycorrhizal fungi (G+ bacteria) compared with saprotrophic fungi (G- bacteria). These changes drove shifts toward fungal-dominated soil microbial communities and then optimized microbial community structure. Also, manure application increased soil biodiversity (microbial community and enzyme function), indicated by increased Shannon-Wiener diversity. Redundancy analysis indicated that the most possible mechanism of the impacts of different fertilization patterns on soil microbial characteristics may be the mediation of SOC and nutrient (N) availability (especially SOC) in this GVP of China. In conclusion, manure substitution of chemical fertilizer, especially at higher substitution rate, was more efficient for improving soil quality and biological functions.

microbiology↗

bioRxiv2019

RanGTP regulates cilium formation and ciliary trafficking of a kinesin-II subunit independent of its nuclear functions

Kinesin is part of the microtubule (MT)-binding motor protein superfamily, which exerts crucial functions in cell division and intracellular transport in different organelles. The heterotrimeric kinesin-II, consisting of the kinesin like protein KIF3A/3B heterodimer and kinesin-associated protein KAP3, is highly conserved across species between the green alga Chlamydomonas and humans. It plays diverse roles in cargo transport including anterograde (base to tip) trafficking in cilium. However, the molecular determinants mediating trafficking of heterotrimeric kinesin-II itself is poorly understood. Using the unicellular eukaryote Chlamydomonas and mammalian cells, we show that RanGTP regulates ciliary trafficking of KAP3. We found the armadillo repeat region 6-9 (ARM6-9) of KAP3, required for its nuclear translocation, is sufficient for its targeting to the ciliary base. Given that KAP3 is essential for cilia formation and the emerging roles of RanGTP/importin {beta} in ciliary protein targeting, we further investigate the effect of RanGTP in cilium length regulation in these two different systems. We demonstrate that precise control of RanGTP levels, revealed by different Ran mutants, is crucial for cilium formation and maintenance. Most importantly, we were able to segregate RanGTP regulation of ciliary protein incorporation from of its nuclear roles. Our work provides important support for the model that nuclear import mechanisms have been coopted for independent roles in ciliary import.

cell biology↗

bioRxiv2019

The Out of East Asia model versus the African Eve model of modern human origins in light of ancient mtDNA findings

The first molecular model of modern human origins published in 1983 had the mtDNA phylogenetic tree rooted in Asia. This model was subsequently overlooked and superseded by the African Eve model in 1987 that was premised on the unrealistic infinite site assumption and the now failed molecular clock hypothesis. We have recently developed a new framework of molecular evolution, the maximum genetic diversity (MGD) hypothesis, which has in turn led us to discover a new model of modern human origins with the roots of uniparental DNAs placed in East Asia. While the African mtDNA Eve model has haplotype N as ancestral to R, our Asia model places R as the ancestor of all. We here examined ancient mtDNAs from the literature focusing on the relationship between N and R. The data showed that all three oldest mtDNAs were R with the 45000 year old Ust-Ishim a basal type and the two ~40000 year old samples sub-branch of R. Among the numerous mtDNAs of 39500-30000 year old, most were R subtype U and only two were N samples, the 39500 year old Oase1 and the 34425 year old Salkhit. These N types are basal and hence likely close to the root of N. These ancient DNA findings suggest that basal R is ~5000 years older than basal N, thereby confirming the East Asia model and invalidating the African Eve model.

evolutionary biology↗

bioRxiv2019

Age and sex-dependent patterns of gut microbial diversity in human adults

Gut microbial diversity changes throughout the human lifespan and is known to be affected by host sex. We investigated the association of age, sex and gut bacterial alpha diversity in three large cohorts of adults from four geographical regions: US and UK cohorts in the American Gut Project, and two independent cohorts of Colombians and Chinese. In three of the four cohorts, we observed a strong positive association between age and alpha diversity in young adults that plateaued after age 40. We also found pronounced sex-dependent differences in younger but not middle-aged adults, and women had higher alpha diversity than men. In contrast, no association of alpha diversity with age or sex was observed in the Chinese cohort. These associations were maintained after adjusting for cardiometabolic parameters in the Colombian cohort and antibiotic usage in the AGP cohort, suggesting that these factors do not affect the association of alpha diversity with age and sex. We also used a machine learning approach to predict individual age based on the gut microbiome. Consistent with our alpha diversity-based findings, women had significantly higher predicted age than men in the US and UK cohort, with a reduced difference above age 40. This was not observed in the Colombian cohort and only in the group of middle-age adults in the Chinese cohort. Together, our results provide new insights into the influence of age and sex on biodiversity of the human gut microbiota during adulthood while highlighting similarities and differences across diverse cohorts.

microbiology↗

bioRxiv2019

Network-specific synchronization of electrical slow-wave oscillations regulates sleep in Drosophila

Slow-wave rhythms characteristic of deep sleep oscillate in the delta band (0.5-4 Hz) and can be found across various brain regions in vertebrates. Across systems it is however unclear how oscillations arise and whether they are the causal functional unit steering behavior. Here, for the first time in any invertebrate, we discover sleep-relevant delta oscillations in Drosophila. We find that slow-wave oscillations in the sleep-regulating R2 network increase with sleep need. Optical multi-unit voltage recordings reveal that single R2 neurons get synchronized by sensory and circadian input pathways. We show that this synchronization depends on NMDA receptor (NMDARs) coincidence detector function and on an interplay of cholinergic and glutamatergic inputs setting a resonance frequency. Genetically targeting the coincidence detector function of NMDARs in R2, and thus the uncovered mechanism underlying synchronization, abolished network-specific slow-wave oscillations. It also disrupted sleep and facilitated light-induced wakening, directly establishing a causal role for slow-wave oscillations in regulating sleep and sensory gating. We therefore propose that the synchronization-based increase in oscillatory power likely represents an evolutionarily conserved, potentially optimal, strategy for constructing sleep-regulating sensory gates.

neuroscience↗

bioRxiv2019

A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases

Prevalence of allergies has reached ~50% of industrialized populations and with children under ten being the most susceptible. However, the combination of the complexity of atopic allergy susceptibility/development and environmental factors has made identification of gene biomarkers challenging. The amount of publicly accessible transcriptomic data presents an unprecedented opportunity for mechanistic discoveries and validation of complex disease signatures across studies. However, this necessitates structured methodologies and visual tools for the interpretation of results. Here, we present a curated collection of transcriptomic datasets relevant to immunoglobin E (IgE)-mediated atopic diseases (ranging from allergies to primary immunodeficiencies). 30 datasets from the Gene Expression Omnibus (GEO), encompassing 1761 transcriptome profiles, were made available on the Gene Expression Browser (GXB), an online and open-source web application that allows for the query, visualization, and annotation of metadata. The thematic compositions, disease categories, sample number, and platforms of the collection are described. Ranked gene lists and sample grouping are used to facilitate data visualization/interpretation and are available online via GXB (http://ige.gxbsidra.org/dm3/geneBrowser/list). Dataset validation using associated publications showed good concordance in GXB gene expression trend and fold-change.\n\nDatabase URL: http://ige.gxbsidra.org/dm3/geneBrowser/list

immunology↗

bioRxiv2018

RNA Polymerase II Independent Recruitment of SPT6 at Transcription Start Sites in Arabidopsis

SPT6 is a conserved transcription regulator that is generally viewed as an elongation factor. However, emerging evidence show its potential role in the control of transcription initiation at genic and intragenic promoters. Here we first present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNA Polymerase II (RNAPII) occupancy across transcribed genes. Further, we show that SPT6L enrichment is shifted, unexpectedly, from gene body to the transcription starting site (TSS) when its association with RNAPII is disrupted. Finally, we demonstrate that recruitment of SPT6L starts at TSS, and then spreads to the gene body during transcription. These findings refine the mechanisms underlying SPT6L recruitment in transcription and shed light on the role of SPT6L in transcription initiation.

molecular biology↗

bioRxiv2018

Rapid active zone remodeling consolidates presynaptic potentiation

Synaptic transmission is mediated by neurotransmitter release at presynaptic active zones (AZs) followed by postsynaptic neurotransmitter detection. Plastic changes in transmission maintain functionality during perturbations and enable memory formation. Postsynaptic plasticity targets neurotransmitter receptors, but presynaptic plasticity mechanisms directly regulating the neurotransmitter release apparatus remain largely enigmatic. Here we describe that AZs consist of nano-modular release site units and identify a molecular sequence adding more modules within minutes of plasticity induction. This requires cognate transport machinery and a discrete subset of AZ scaffold proteins. Structural remodeling is not required for the immediate potentiation of neurotransmitter release, but rather necessary to sustain this potentiation over longer timescales. Finally, mutations in Unc13 that disrupt homeostatic plasticity at the neuromuscular junction also impair shot-term memory when central neurons are targeted, suggesting that both forms of plasticity operate via Unc13. Together, while immediate synaptic potentiation capitalizes on available material, it triggers the coincident incorporation of modular release sites to consolidate stable synapse function.

neuroscience↗

bioRxiv2018

Ancient DNAs and the Neolithic Chinese super-grandfather Y haplotypes

Previous studies identified 3 Neolithic Han Chinese super-grandfather Y haplotypes, O2a2b1a1a-F5, O2a2b1a2a1-F46, and O2a1b1a1a1a-F11, but their relationships with the archaeological and written records remain unexplored. We here report genome wide DNA data for 12 ancient samples (0.02x-1.28x) from China ranging from 6500 to 2500 years before present (YBP). They belonged to 4 different genetic groups, designated as Dashanqian (DSQ) of Xiajiadian Culture in the Northeast, Banpo (BP) of middle Yangshao Culture in the Central West, Zhengzhou Xishan (ZX) of Miaodigou Culture in the Central Plains, and Others. Present day F5 samples were closer in autosomal distances to the ZX and DSQ groups while F11, C, O1, and O2 samples were closer to the BP group. We also sequenced the Y chromosome of one of these ancient samples K12 from DSQ and found both K12 and a previously reported ~4000 year old sample MG48 from Northwest China to have the O2a2b1a1a1a2a-F2137 haplotype, belonging to the most prolific branch O2a2b1a1a1-F438 immediately under F5. We further found close relationships between ZX and DSQ and between ZX and ancient M117 Tibetans or present day Southwest Dai Chinese carrying the F5 subtype O2a2b1a1a6, implicating radiations of F5 subtypes from the putative place of F5 origin in ZX. These results are remarkably consistent with archaeological and written records.

evolutionary biology↗

bioRxiv2018

Pan-cancer analysis on microRNA-mediated gene activation

While microRNAs (miRNAs) were widely considered to repress target genes at mRNA and/or protein levels, emerging evidence from in vitro experiments has shown that miRNAs can also activate gene expression in particular contexts. However, this counterintuitive observation has rarely been reported or interpreted in in vivo conditions. We systematically explored the positive correlation between miRNA and gene expressions and its potential implications in tumorigenesis, based on 8375 patient samples across 31 major human cancers from The Cancer Genome Atlas (TCGA). Results indicated that positive miRNA-gene correlations are surprisingly prevalent and consistent across cancer types, and show distinct patterns than negative correlations. The top-ranked positive correlations are significantly involved in the immune cell differentiation and cell membrane signaling related processes, and display strong power in stratifying patients in terms of survival rate, demonstrating their promising clinical relevance. Although intragenic miRNAs generally tend to co-express with their host genes, a substantial portion of miRNAs shows no obvious correlation with their host gene due to non-conservation. A miRNA can upregulate a gene by inhibiting its upstream suppressor, or shares transcription factors with that gene, both leading to positive correlation. The miRNA/gene sites associated with the top-ranked positive correlations are more likely to form super-enhancers compared to randomly chosen pairs, suggesting a potential epigenetics mechanism underlying the upregulation. Wet-lab experiments revealed that positive correlations partially remain in the in vitro condition. Our study provides the field with new perspectives on the critical role of miRNA in gene regulation and novel insights regarding the complex mechanisms underlying miRNA functions, and reveals the clinical significance of the potential positive regulation of gene expression by miRNA.

bioinformatics↗