Biology subjects

Huang, X.

Publications and source records attributed to Huang, X..

31 records · Page 2Linked to original sources

bioRxiv2018

Establishment of signaling interactions with cellular resolution for every cell cycle of embryogenesis

Intercellular signaling interaction plays a key role in breaking fate symmetry during animal development. Identification of the signaling interaction at cellular resolution is technically challenging, especially in a developing embryo. Here we develop a platform that allows automated inference and validation of signaling interaction for every cell cycle of C. elegans embryogenesis. This is achieved by generation of a systems-level cell contact map that consists of 1,114 highly confident intercellular contacts by modeling analysis and is validated through cell membrane labeling coupled with cell lineage analysis. We apply the map to identify cell pairs between which a Notch signaling interaction takes place. By generating expression patterns for two ligands and two receptors of Notch signaling pathway with cellular resolution using automated expression profiling technique, we are able to refine existing and identify novel Notch interactions during C. elegans embryogenesis. Targeted cell ablation followed by cell lineage analysis demonstrates the roles of signaling interactions over cell division in breaking fate symmetry. We finally develop a website that allows online access to the cell-cell contact map for mapping of other signaling interaction in the community. The platform can be adapted to establish cellular interaction from any other signaling pathways.

cell biology↗

bioRxiv2018

The UBR-1 Ubiquitin Ligase Regulates Glutamate Metabolism to Generate Coordinated Motor Pattern in C. elegans

UBR1 is an E3 ubiquitin ligase best known for its ability to target protein degradation by the N-end rule. The physiological functions of UBR family proteins, however, remain not fully understood. We found that the functional loss of C. elegans UBR-1 leads to a specific motor deficit: when adult animals generate reversal movements, A-class motor neurons exhibit synchronized activation, preventing body bending. This motor deficit is rescued by removing GOT-1, a transaminase that converts aspartate to glutamate. Both UBR-1 and GOT-1 are expressed and critically required in premotor interneurons of the reversal motor circuit to regulate the motor pattern. ubr-1 and got-1 mutants exhibit elevated and decreased glutamate level, respectively. These results raise an intriguing possibility that UBR proteins regulate glutamate metabolism, which is critical for neuronal development and signaling.\n\nAuthor SummaryUbiquitin-mediated protein degradation is central to diverse biological processes. The selection of substrates for degradation is carried out by the E3 ubiquitin ligases, which target specific groups of proteins for ubiquitination. The human genome encodes hundreds of E3 ligases; many exhibit sequence conservation across animal species, including one such ligase called UBR1. Patients carrying mutations in UBR1 exhibit severe systemic defects, but the biology behinds UBR1s physiological function remains elusive. Here we found that the C. elegans UBR-1 regulates glutamate level. When UBR-1 is defective, C. elegans exhibits increased glutamate; this leads to synchronization of motor neuron activity, hence defective locomotion when animals reach adulthood. UBR1-mediated glutamate metabolism may contribute to the physiological defects of UBR1 mutations.

neuroscience↗

bioRxiv2018

A Convenient Non-harm Cervical Spondylosis Intelligent Identity method based on Machine Learning

Cervical spondylosis(CS), a most common orthopedic diseases, is mainly identified by the doctors judgment from the clinical symptoms and cervical change provided by expensive instruments in hospital. Owing to the development of the surface electromyography(sEMG) technique and artificial intelligence, we proposed a convenient non-harm CS intelligent identify method EasiCNCSII, including the sEMG data acquisition and the CS identification. For the convenience and efficiency of data acquisition with the limited testable muscles provided by the sEMG technology, we proposed a data acquisition method based on the relationship between muscle activity pattern, the tendons theory and CS etiology. It is easily performed in less than 20 minutes, even outside the hospital. Faced with the challenge of high-dimension and the weak availability, the 3-tier model EasiAI is developed to intelligently identify CS. The common features and new features are extracted from raw sEMG data in first tier. The EasiRF is proposed in second tier to further reduce the data dimension and improve the performance. With the limited and weakly available data, the gradient boosted regression tree is developed in third tier to effectively identify CS. The EasiAI achieve the best performance with 91.02% in accuracy, 97.14% in sensitivity, and 81.43% in specificity compared with 4 common machine learning classification model, validating the EasiCNCSII effectiveness.

bioinformatics↗

bioRxiv2018

AMPKi overcomes the paradoxical activation of CRAF driven by RAF inhibitors through blocking the 14-3-3 binding to its carboxyl-terminus

The paradoxical activation of RAF kinase is the predominant challenge in cancer therapies with RAF inhibitors. The inhibitor-bound RAF molecules are able to transactivate their wild-type binding partners. 14-3-3 that binds to the carboxyl-terminus of RAF kinase has been suggested to regulate the dimer-dependent activation of RAF kinase under physiological conditions, though the molecular basis is not clear. In this study, we investigated the role of 14-3-3 in the paradoxical effect of RAF inhibitors. Firstly, we found that the 14-3-3 binding to the carboxyl-terminus of CRAF was essential for its transactivation. Further, we demonstrated that this binding enhanced the dimer affinity of CRAF. Since 14-3-3 binds to the phosphorylated motif, we next investigated and identified AMPK and CRAF itself as two putative kinases that phosphorylate redundantly the 14-3-3 binding motif of CRAF. Among RAF isoforms, CRAF plays a dominant role in the paradoxical effect of RAF inhibitors, and we thus determined whether the combinatory inhibition of AMPK and CRAF would block this effect. Indeed, our data showed that AMPKi not only blocked the RAF inhibitor-driven paradoxical activation of RAF signaling and cellular overgrowth in Ras-mutated cancer cells but also reduced the drug-resistant clones derived from BRAF(V600E)-mutated cancer cells. Finally, we showed that the 14-3-3 binding to the carboxyl-terminus of CRAF was dispensable for its catalytic function in vivo. Together, our study unraveled how 14-3-3 regulates the dimerization-driven RAF activation and identified AMPKi as a potential method to relieve the drug resistance and side effect of RAF inhibitors in cancer therapy.

cancer biology↗

bioRxiv2018

Dissecting historical changes of selective pressures in the evolution of human pigmentation

Human pigmentation is a highly diverse and complex trait among populations, and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We propose a new model with multiple populations to estimate historical selective pressures by summarizing selective pressures on multiple genes. We use genotype data of 19 genes associated with human pigmentation from 17 datasets, and obtain data for 2346 individuals of six representative population groups from worldwide. Our results quantify selective pressures on light pigmentation not only in modern Europeans (0.0249/generation) but also in proto-Eurasians (0.00665/generation). Our results also support several derived alleles associated with human dark pigmentation may under directional selection by quantifying differences of selective pressures between populations. Our study provides a first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation, and may facilitate studies of the evolution of other complex traits.\n\nAuthor SummaryThe color variation of human skin, hair, and eye is affected by multiple genes with different roles. This diversity may be shaped by natural selection and adapted for ultraviolet radiation in different environments around the world. As human populations migrated out from Africa, the ultraviolet radiation in the environment they encountered also changed. It is possible that the selective pressures on human pigmentation varied throughout human evolutionary history. In this study, we develop a new approach and estimate historical selective pressures on light pigmentation not only in modern Europeans but also in proto-Eurasians. To our best knowledge, this is the first study that quantifies selective pressures during different time periods in the evolution of human pigmentation. Besides, we provide statistical evidence to support several genes associated with human dark pigmentation may be favored by natural selection. Thus, natural selection may not only affect light pigmentation in Eurasians, but also influence dark pigmentation in Africans.

evolutionary biology↗

bioRxiv2017

A Cell Type-Specific Class of Chromatin Loops Anchored at Large DNA Methylation Nadirs

Higher order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we found that large (~10kb) DNA methylation nadirs can form long loops connecting anchor loci that may be dozens of megabases apart, as well as interchromosomal links. The interacting loci comprise ~3.5Mb of the human genome. The data are more consistent with the formation of these loops by phase separation of the interacting loci to form a genomic subcompartment, rather than with CTCF-mediated extrusion. Interestingly, unlike previously characterized genomic subcompartments, this subcompartment is only present in particular cell types, such as stem and progenitor cells. Further, we identify one particular loop anchor that is functionally associated with maintenance of the hematopoietic stem cell state. Our work reveals that H3K27me3-marked large DNA methylation nadirs represent a novel set of very long-range loops and links associated with cellular identity.\n\nSummaryHi-C and DNA methylation analyses reveal novel chromatin loops between distant sites implicated in stem and progenitor cell function.

genomics↗

bioRxiv2017

runibic: a Bioconductor package for parallel row-based biclustering of gene expression data

MotivationBiclustering (called also co-clustering) is an unsupervised technique of simultaneous analysis of rows and columns of input matrix. From the first application to gene expression data, multiple algorithms have been proposed. Only a handful of them were able to provide accurate results and were fast enough to be suitable for large-scale genomic datasets.\n\nResultsIn this paper we introduce a Bioconductor package with parallel version of UniBic biclustering algorithm: one of the most accurate biclustering methods that have been developed so far. For the convenience of usage, we have wrapped the algorithm in an R package called runibic. The package includes: (1) a couple of times faster parallel version of the original sequential algorithm,(2) muchmore efficient memory management, (3) modularity which allows to build new methods on top of the provided one, (4) integration with the modern Bioconductor packages such as SummarizedExperiment, ExpressionSetand biclust.\n\nAvailabilityThe package is implemented in R (3.4) and will be available in the new release of Bioconductor (3.6). Currently it could be downloaded from the following URL: http://github.com/athril/runibic/\n\nContactpatryk.orzechowski@gmail.com, jhmoore@upenn.edu\n\nSupplementary informationSupplementary informations are available in vignette of the package.

bioinformatics↗

bioRxiv2017

Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA

DksA and ppGpp are the central players in the Escherichia coli stringent response and mediate a complete reprogramming of the transcriptome from one optimized for rapid growth to one adapted for survival during nutrient limitation. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of E. coli RNAP holoenzyme in complex with DksA alone and with ppGpp. The structures show that DksA accesses the template strand at the active site and the downstream DNA binding site of RNAP simultaneously and reveal that binding of the allosteric effector ppGpp reshapes the RNAP-DksA complex. The structural data support a model for transcriptional inhibition in which ppGpp potentiates the destabilization of open complexes on rRNA promoters by DksA. We also determined the structure of RNAP-TraR complex, which reveals the mechanism of ppGpp-independent transcription inhibition by TraR. This work establishes new ground for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria.\n\nHighlightsO_LIDksA has two modes of binding to RNA polymerase\nC_LIO_LIDksA is capable of inhibiting the catalysis and influences the DNA binding of RNAP\nC_LIO_LIppGpp acts as an allosteric effector of DksA function\nC_LIO_LIppGpp stabilizes DksA in a more functionally important binding mode\nC_LI

molecular biology↗

bioRxiv2017

The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology

Pomegranate (Punica granatum L.) with an uncertain taxonomic status has an ancient cultivation history, and has become an emerging fruit due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the absence of genomic resources has restricted further elucidating genetics and evolution of these interesting traits. Here we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336 Mb genome, consists of 2,177 scaffolds with an N50 size of 1.7 Mb, and contains 30,903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis shares the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the color formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence represents the first reference in Lythraceae, providing an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.

genomics↗

bioRxiv2017

Cohesin Loss Eliminates All Loop Domains, Leading To Links Among Superenhancers And Downregulation Of Nearby Genes

The human genome folds to create thousands of intervals, called \"contact domains,\" that exhibit enhanced contact frequency within themselves. \"Loop domains\" form because of tethering between two loci - almost always bound by CTCF and cohesin - lying on the same chromosome. \"Compartment domains\" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loci in different compartments that had been in the same loop domain become more segregated. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. Cohesin restoration quickly reverses these effects, consistent with a model where loop extrusion is rapid.

genomics↗

bioRxiv2017

Ultra-Accurate Genome Sequencing And Haplotyping Of Single Human Cells

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (Single-Stranded Sequencing using micrOfluidic Reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10-8 and average 500kb long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs.

genomics↗

bioRxiv2017

Detecting Presence Of Mutational Signatures In Cancer With Confidence

Cancers arise as the result of somatically acquired changes in the DNA of cancer cells. However, in addition to the mutations that confer a growth advantage, cancer genomes accumulate a large number of somatic mutations resulting from normal DNA damage and repair processes as well as mutations triggered by carcinogenic exposures or cancer related aberrations of DNA mainte-nance machinery. These mutagenic processes often produce characteristic mutational patterns called mutational signatures. Decomposition of cancers mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology. However, the results from di[ff]erent decomposition methods are not always consistent. Hence, one needs to not only be able to decompose a patients mutational profile into signatures but also to establish the accuracy of such decomposition. We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes. We identified very stable and highly unstable signatures, as well as signatures that have been missed altogether. We also provided additional support for the novel signatures. Our results emphasize the importance of assessing the confidence and stability of inferred signature contributions. All tools developed in this paper have been implemented in an R package, called SignatureEstimation, which is available from https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#signatureestimation.

bioinformatics↗

bioRxiv2017

High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

SynopsisO_ST_ABSBackgroundC_ST_ABSmcr-1-mediated transmissible colistin resistance in Enterobacteriaceae is concerning, given colistin is frequently used as a treatment of last resort in multidrug-resistant Enterobacteriaceae infections. Reported rates of human mcr-1 gastrointestinal carriage have historically been low.\n\nObjectivesTo identify trends in human gastrointestinal carriage of mcr-1 positive and mcr-1-positive/cefotaxime-resistant Enterobacteriaceae in Guangzhou, China, 2011-2016, and investigate the genetic contexts of mcr-1 in a subset of mcr-1-positive/cefotaxime-resistant strains using whole genome sequencing (WGS).\n\nMethodsOf 8,022 faecal samples collected, 497 (6.2%) were mcr-1- positive, and 182 (2.3%) mcr-1-positive/cefotaxime-resistant. Trends in carriage were assessed using iterative sequential regression. A subset of mcr-1-positive isolates was sequenced (Illumina), and genetic contexts of mcr-1 were characterised.\n\nResultsWe observed marked increases in mcr-1 (now ~30% prevalence) and more recent (since January 2014) increases in mcr-1-positive/third-generation cephalosporin-resistant Enterobacteriaceae human colonisation (p<0.001). Sub-cultured mcr-1-positive/third-generation cephalosporin-resistant isolates were commonly multi-drug resistant.\n\nWGS of 50 mcr-1/third-generation cephalosporin-resistant isolates (49 Escherichia coli; 1 Klebsiella pneumoniae) demonstrated bacterial strain diversity (39 E. coli sequence types); mcr-1 in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequent mcr-1 chromosomal integration; and loss of the mcr-1-associated insertion sequence ISApl1 in some plasmids. Significant sequence similarity with published mcr-1 plasmid sequences was consistent with spread amongst pig, chicken and human reservoirs.\n\nConclusionsThe high positivity rate (~10%) of mcr-1 in multidrug-resistant E. coli colonising humans is a clinical threat; the diverse genetic mechanisms (strains/plasmids/insertion sequences) associated with mcr-1 have likely contributed to its dissemination, and will facilitate its persistence.

microbiology↗