Biology subjects

Xu, J.

Publications and source records attributed to Xu, J..

At least 847 records · Page 47Linked to original sources

bioRxiv2019

Deep protein methylation profiling by combined chemical and immunoaffinity approaches reveals novel PRMT1 targets

Protein methylation has been implicated in many important biological contexts including signaling, metabolism, and transcriptional control. Despite the importance of this post-translational modification, the global analysis of protein methylation by mass spectrometry-based proteomics has not been extensively studied due to the lack of robust, well-characterized techniques for methyl peptide enrichment. Here, to better investigate protein methylation, we optimized and compared two methods for methyl peptide enrichment: immunoaffinity purification (IAP) and high pH strong cation exchange (SCX). Comparison of these methods revealed that they are largely orthogonal for monomethyl arginine (MMA), suggesting that the usage of both techniques is required to provide a global view of protein methylation. Using both IAP and SCX, we investigated changes in protein methylation downstream of protein arginine methyltransferase 1 (PRMT1) and quantified [~]1,000 methylation sites on 407 proteins. Of these methylation sites, PRMT1 knockdown resulted in significant changes to 97 arginine methylation sites on 59 proteins. In contrast, zero lysine methylation sites were significantly changed upon PRMT1 knockdown. In PRMT1 knockdown cells, 84 MMA sites were either significantly downregulated or upregulated. PRMT1 knockdown also induced significant changes in both asymmetric dimethyl arginine (ADMA) and symmetric dimethyl arginine (SDMA), suggesting that loss of PRMT1 activity allows scavenging of PRMT1 substrates by other PRMTs. Using neutral loss fragmentation ions unique to ADMA and SDMA, we annotated dimethylarginines as either ADMA or SDMA. Through integrative analysis of methyl forms, we identified 12 high confidence PRMT1 substrates, 43 putative PRMT1 substrates, and 17 methylation sites that are scavenged by other non-PRMT1 arginine methyltransferases in the absence of PRMT1 activity. Taken together, our results suggest that deep protein methylation profiling by mass spectrometry requires orthogonal enrichment techniques to identify novel PRMT1 methylation targets and highlight the dynamic interplay between methyltransferases in mammalian cells.

systems biology↗

bioRxiv2019

Formalin Tissue Fixation Biases Myelin-Sensitive MRI

PurposeChemical fixatives, such as formalin, form cross-links between proteins and affect the relaxation times and diffusion properties of tissue. These fixation-induced changes likely also affect myelin density measurements produced by quantitative magnetization transfer (qMT) and myelin water imaging (MWI). In this work, we evaluate these myelin-sensitive MRI methods for fixation-induced biases. MethodsWe perform qMT, MWI, and D2O-exchanged zero echo-time (ZTE) imaging on unfixed human spinal cord tissue, and repeat these measurements after 1 day and 31 days of formalin fixation. ResultsThe qMT bound pool fraction increased by 30.7{+/-}21.1% after 1 day of fixation and by 42.6{+/-}33.9% after 31 days of fixation. Myelin water fraction increased by 39.7{+/-}15.5% and 37.0{+/-}15.9% at these same time points, and mean T2 of the myelin water pool nearly doubled. Reference-normalized D2O-exchanged ZTE signal intensity increased by 8.17{+/-}6.03% after 31 days of fixation, but did not change significantly after 1 day of fixation. After fixation, specimen cross-sectional area decreased by approximately 5%; after correction for shrinkage, changes in D2O-exchanged ZTE intensity were nearly eliminated. ConclusionF and MWF are significantly increased by formalin fixation, while D2O-exchanged ZTE intensity is minimally affected. Changes in qMT and MWI may be due, in part, to delamination and formation of vacuoles in the myelin sheath. D2O-exchanged signal intensity may be altered by fixation-induced changes in myelin lipid solid-state 1H T1. We urge caution in the comparison of these measurements across subjects or specimens in different states, especially unfixed vs. fixed tissue.

neuroscience↗

bioRxiv2019

Requirement for TRanslocon-Associated Protein (TRAP) α in insulin biogenesis

The mechanistic basis for the biogenesis of peptide hormones and growth factors is poorly understood. Here we show that the conserved endoplasmic reticulum (ER) membrane translocon-associated protein (TRAP) , also known as signal sequence receptor 1 (SSR1)1, plays a critical role in the biosynthesis of insulin. A genetic screen in the nematode Caenorhabditis elegans revealed trap-1, which encodes the C. elegans TRAP ortholog, as a modifier of DAF-2 insulin receptor (InsR) signaling. Genetic analysis indicates that TRAP-1 acts upstream of DAF-2/InsR to control C. elegans development. Endogenous C. elegans TRAP-1 and mammalian TRAP both localized to the ER. In pancreatic beta cells, TRAP deletion impaired preproinsulin translocation but did not affect the synthesis of 1-antitrypsin, indicating that TRAP selectively influences the translocation of a subset of secreted proteins. Surprisingly, loss of TRAP function also resulted in disruption of distal steps in insulin biogenesis including proinsulin processing and secretion. These results show that TRAP assists in the ER translocation of preproinsulin and unveil unanticipated additional consequences of TRAP loss-of-function on the intracellular trafficking and maturation of proinsulin. The association of common intronic single nucleotide variants in the human TRAP gene with susceptibility to Type 2 diabetes and pancreatic beta cell dysfunction2 suggests that impairment of preproinsulin translocation and proinsulin trafficking may contribute to the pathogenesis of Type 2 diabetes.

genetics↗

bioRxiv2019

Changes in fungal communities across a forest disturbance gradient

Deforestation has a substantial impact on above ground biodiversity, but the response of below ground soil fungi remains poorly understood. In a tropical montane rainforest in southwestern China, plots were established along a forest degradation gradient ranging from mature and regenerated forests to open land to examine the impacts of forest degradation and deforestation on ecosystem diversity and function. Here, we evaluate the changes in below ground fungal diversity and community composition using a metabarcoding approach. Soil saprotrophic fungal richness declined with increasing forest disturbance. For example, Penicillium spp. (Phosphorus (P) solubilizing fungi) dominated in mature forest, but were less abundant in regenerating forest and showed the lowest abundance in open land sites. Conversely, the abundance of facultative pathogenic fungi increased along the disturbance gradient. The decline in soil saprophytic fungi may be a direct result of forest disturbance or it may be associated with increased availability of soil phosphorus indirectly through an increase in soil pH. The increase in abundance of facultative pathogenic fungi may be related to reduce competition with saprotrophic fungi, changes in microclimate or increased spore rain. These results demonstrate a loss of dominant P solubilizing saprotrophic fungi along the disturbance gradient, indicated a change from soil P limitation in mature tropical forest to soil C limitation in deforested sites. The increased prevalence of pathogenic fungi may inhibit plant succession following deforestation. Overall, this research demonstrates that soil fungi can be used as a sensitive indicator for soil health to evaluate the consequences of forest disturbance.\n\nImportanceThe soil fungal functional group changes in response to forest disturbance indicated a close interaction between the above-ground plant community and the below-ground soil biological community. Soil saprotrophic fungi declined in relative abundance with increasing forest disturbance. At the same time, the relative abundance of facultative pathogenic fungi increased. The loss of saprotrophic fungal richness and abundance may have been a direct result of forest disturbance or an indirect result of changes in soil pH and soil P. Furthermore, the dominant P solubilizing saprotrophic fungi was replaced by diverse facultative pathogenic fungi, which have weaker C decomposition ability. These changes potentially indicate a shift from soil phosphate limitation to carbon limitation following deforestation. This study suggests that changes in fungal functional group composition can be used as an indicator of the effects of forest disturbance on soil carbon and nutrients.

ecology↗

bioRxiv2019

Contribution of pretomanid to novel regimens containing bedaquiline with either linezolid or moxifloxacin and pyrazinamide in murine models of tuberculosis

Novel regimens combining bedaquiline and pretomanid with either linezolid (BPaL regimen) or moxifloxacin and pyrazinamide (BPaMZ regimen) shorten the treatment duration needed to cure TB in BALB/c mice compared to the first-line regimen and have yielded promising results in initial clinical trials. However, the independent contribution of the investigational new drug pretomanid to the efficacy of BPaMZ has not been examined and its contribution to BPaL has been examined only over the first 2 months of treatment. In the present study, the addition of pretomanid to BL increased bactericidal activity, prevented emergence of bedaquiline resistance, and shortened the duration needed to prevent relapse with drug-susceptible isolates by at least 2 months in BALB/c mice. Addition of pretomanid to BMZ resulted in a 1 log10 greater CFU reduction after 1 month of treatment and/or reduced the number of mice relapsing in each of 2 experiments in BALB/c mice and in immunocompromised nude mice. Bedaquiline-resistant isolates were found at relapse in only one BMZ-treated nude mouse. Treatment of infection with a pyrazinamide-resistant mutant in BALB/c mice with BPaMZ prevented selection of bedaquiline-resistant mutants and reduced the proportion of mice relapsing compared to BMZ alone. Among severely ill C3HeB/FeJ mice with caseous pneumonia and cavitation, BPaMZ increased median survival ([≥]60 vs. 21 days) and reduced median lung CFU by 2.4 log10 at 1 month compared to BMZ. In conclusion, in 3 different mouse models, pretomanid contributed significantly to the efficacy of the BPaMZ and BPaL regimens, including restricting the selection of bedaquiline-resistant mutants.

pharmacology and toxicology↗

bioRxiv2018

The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio

Common carp (Cyprinus carpio) is an allotetraploid Cyprinid species derived from recent whole genome duplication and provides an excellent model system for studying polyploid genome evolution in vertebrates. To explore the origins and consequences of tetraploidy in C. carpio, we generated three chromosome-level new reference genomes of C. carpio and compared them to the related diploid Cyprinid genome sequences. We identified a progenitor-like diploid Barbinae lineage by analysing the phylogenetic relationship of the homoeologous genes of C. carpio and their orthologues in closely related diploid Cyprinids. We then characterized the allotetraploid origin of C. carpio and divided its genome into two homoeologous subgenomes that are marked by a distinct genome similarity to their diploid progenitor. On the basis of the divergence rates of homoeologous genes and transposable elements in two subgenomes, we estimated that the two diploid progenitor species diverged approximately 23 million years ago (Mya) and merged to form the allotetraploid C. carpio approximately 12.4 Mya, which likely correlated with environmental upheavals caused by the extensive uplift of the Qinghai-Tibetan Plateau. No large-scale gene losses or rediploidization were observed in the two subgenomes. Instead, we found extensive homoeologous gene expression bias across twelve surveyed tissues, which indicates that subgenome B is dominant in homoeologous expression. DNA methylation analysis suggested that CG methylation in promoter regions plays an important role in altering the expression of these homoeologous genes in allotetraploid C. carpio. This study provides an essential genome resource and insights for extending further investigation on the evolutionary consequences of vertebrate polyploidy.

genomics↗

bioRxiv2018

Identification of TTN as a novel candidate gene for atrioventricular block in a Chinese pedigree by whole-exome sequencing

PurposeCardiovascular diseases are the most common cause of death globally. In which atrioventricular block (AVB) is a common disorder with genetic causes, but the responsible genes have not been fully identified yet. To determine the underlying causative genes involved in cardiac AVB, here we report a three-generation Chinese family with severe autosomal dominant cardiac AVB that has been ruled out as being caused by known genes mutations.\n\nMethodsWhole-exome sequencing was performed in five affected family members across three generations, and co-segregation analysis was validated on other members of this family.\n\nResultsWhole-exome sequencing and subsequent co-segregation validation identified a novel germline heterozygous point missense mutation, c.49287C>A (p.N16429K), in the titin (TTN, NM_001267550.2) gene in all 5 affected family members, but not in the unaffected family members. The point mutation is predicted to be functionally deleterious by in-silico software tools. Our finding was further supported by the conservative analysis across species.\n\nConclusionBased on this study, TTN was identified as a potential novel candidate gene for autosomal dominant AVB; this study expands the mutational spectrum of TTN gene and is the first to implicate TTN mutations as AVB disease causing in a Chinese pedigree.

genetics↗

bioRxiv2018

Access COI barcode efficiently using high throughput Single End 400 bp sequencing

O_LIOver the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, constraints in barcoding costs led to unbalanced efforts which prevented accurate taxonomic identification for biodiversity studies.\nC_LIO_LIWe present a high throughput sequencing approach based on the HIFI-SE pipeline which takes advantage of Single-End 400 bp (SE400) sequencing data generated by BGISEQ-500 to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons. HIFI-SE was written in Python and included four function modules of filter, assign, assembly and taxonomy.\nC_LIO_LIWe applied the HIFI-SE to a test plate which contained 96 samples (30 corals, 64 insects and 2 blank controls) and delivered a total of 86 fully assembled HIFI COI barcodes. By comparing to their corresponding Sanger sequences (72 sequences available), it showed that most of the samples (98.61%, 71/72) were correctly and accurately assembled, including 46 samples that had a similarity of 100% and 25 of ca. 99%.\nC_LIO_LIOur approach can produce standard full-length barcodes cost efficiently, allowing DNA barcoding for global biomes which will advance DNA-based species identification for various ecosystems and improve quarantine biosecurity efforts.\nC_LI

ecology↗

bioRxiv2018

Robust Antibacterial Activity of Tungsten Oxide (WO3-X) Nanodots

Antibacterial agents are an important tool in the prevention of bacterial infections. Inorganic materials are attractive due to their high stability under a variety of conditions compared to organic antibacterial agents. Herein tungsten oxide nanodots (WO3-X), synthesized by a simple one-pot synthetic approach, was found to exhibit efficient antibacterial capabilities. The analyses with colony-forming units (CFU) showed excellent antibacterial activity of WO3-X against both gram-negative E. coli (Escherichia coli) and gram-positive S. aureus (Staphylococcus aureus) strains. The scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images revealed clear damage to the bacterial cell membranes, which was further confirmed by molecular dynamics simulations. Additionally, exposure to simulated sunlight was found to further increase germicidal activity of WO3-X nanodots - a 30-minute exposure to sunlight (combining 50 g/mL WO3-X nanodots) showed a 70% decrease in E. coli viability compared to without exposure. Electron spin resonance spectroscopy (ESR) was used to elucidate the underlying mechanism of this photocatalytic activity through the generation of hydroxyl radical species. Cell counting kit-8 (CCK-8) and the live/dead assay were further employed to evaluate the cytotoxicity of WO3-X nanodots on eukaryotic cells, which demonstrated their general biocompatibility. In all, our results suggest WO3-X nanodots have considerable potential in antibacterial applications, while also being biocompatible at large.

pharmacology and toxicology↗

bioRxiv2018

Comparative Transcriptomes Analysis of Taenia pisiformis at Different Development Stages

To understand the characteristics of the transcriptional group of Taenia pisiformis at different developmental stages, and to lay the foundation for the screening of vaccine antigens and drug target genes, the transcriptomes of adult and larva of T. pisiformis were assembled and analyzed using bioinformatic tools. A total of 36,951 unigenes with a mean length of 950bp were formed, among which 12,665, 8,188, 7,577, and 6,293 unigenes have been annotated respectively by sequence similarity analysis with four databases (NR, Swiss-Prot, KOG, and KEGG). It should be noted there are 5,662 unigenes that share good similarity with the four databases and get a relatively perfect functional annotation. Besides, a total of 10,247 differentially expressed genes were screened. To be specific, 6,910 unigenes were up-regulated in the larva stage while 3,337 were down-regulated in the adult stage. To sum up, this study sequenced and analyzed the transcriptomes of the larval and adult stages of T. pisiformis. The results of differentially expressed genes in these two stages could provide basis for functional genomics, immunology and gene expression profiles of T. pisiformis.

molecular biology↗

bioRxiv2018

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

Simultaneous measurement of cell lineage and cell fates is a longstanding goal in biomedicine. Here we describe EMBLEM, a strategy to track cell lineage using endogenous mitochondrial DNA variants in ATAC-seq data. We show that somatic mutations in mitochondrial DNA can reconstruct cell lineage relationships at single cell resolution with high sensitivity and specificity. Using EMBLEM, we define the genetic and epigenomic clonal evolution of hematopoietic stem cells and their progenies in patients with acute myeloid leukemia. EMBLEM extends lineage tracing to any eukaryotic organism without genetic engineering.

genomics↗

bioRxiv2018

Beyond a ribosomal RNA methyltransferase, the wider role of MraW in DNA methylation, motility and colonization in Escherichia coli O157:H7

MraW (RsmH) is an AdoMet-dependent 16S rRNA methyltransferase conserved in bacteria and plays a role in the fine-tuning of the ribosomal decoding center. It was recently found to contribute to the virulence of Staphylococcus aureus in host animals. In this study, we examined the function of MraW in Escherichia coli O157:H7 and found that deletion of mraW led to decreased motility and flagellar production. Whole-genome bisulfite sequencing showed genome wide decrease of methylation of 336 genes and 219 promoters in the mraW mutant. The methylation level of 4 flagellar gene sequences were further confirmed by bisulfite PCR sequencing. Quantitative reverse transcription PCR results indicated the transcription of these genes was also affected. MraW was observed to directly bind to the four flagellar gene sequences by electrophoretic mobility shift assay (EMSA). A common motif in differentially methylated regions of promoters and coding regions of the 4 flagellar genes was identified. Reduced methylation was correlated with altered expression of 21 of the 24 genes tested. DNA methylation activity of MraW was confirmed by DNA methyltransferase (DNMT) activity assay in vitro. The mraW mutant colonized poorer than wild type in mice. we further found that the expression of mraZ in the mraW mutant was increased confirming the antagonistic effect of mraW on mraZ. In conclusion, mraW was found to be a DNA methylase and has a wide-ranging effect on E. coli O157:H7 including motility and virulence in vivo via genome wide methylation and mraZ antagonism.\n\nIMPORTANCEMraW is a well-studied 16S rRNA methyltransferase and was recently found have an impact on bacterial virulence. Here we demonstrated its new function as a DNA methylase and effect on motility, colonization in mice, DNA methylation in genome wide and contribution to virulence. Its direct binding of differentially methylated flagellar-encoding DNA sequences was observed, indicating a correlation between DNA methylation and regulation of flagellar genes. In addition, the expression of mraZ which function as an antagonist of mraW was increased in the mraW mutant. mraW plays an important role in gene regulation likely through DNA methylation. Clearly it plays a role in virulence in E. coli O157:H7. It also opens a new research field for virulence study in bacteria.

microbiology↗

bioRxiv2018

GRAM: A generalized model to predict the molecular effect of a non-coding variant in a cell-type specific manner

There has been much effort to prioritize genomic variants with respect to their impact on \"function\". However, function is often not precisely defined: Sometimes, it is the disease association of a variant; other times, it reflects a molecular effect on transcription or epigenetics. Here we coupled multiple genomic predictors to build GRAM, a generalized model, to predict a well-defined experimental target: the expression-modulating effect of a non-coding variant in a cell-specific manner. As a first step, we performed feature engineering: using a LASSO regularized linear model, we found transcription factor (TF) binding most predictive, especially for TFs that are hubs in the regulatory network; in contrast, evolutionary conservation, a popular feature in many other functional-impact predictors, has almost no contribution. Moreover, TF binding inferred from in vitro SELEX is as effective as that from in vivo ChIP-Seq. Second, we implemented GRAM integrating SELEX features and expression profiles. The program combines a universal regulatory score for a variant in a non-coding element with a modifier score reflecting the particular cell type. We benchmarked GRAM on a large-scale MPRA dataset in the GM12878 cell line, achieving a ROC score of [~]0.73; performance on the K562 cell line was similar. Finally, we evaluated the performance of GRAM on targeted regions using luciferase assays in MCF7 and K562 cell lines. We noted that changing the insertion position of the construct relative to the reporter gene gives very different results, highlighting the importance of carefully defining the functional target the model is predicting.\n\nAuthor SummaryNoncoding variants lie outside of protein-coding regions, and are found to have disease associations. However, knowledge on the molecular effect of these non-coding variants in a cell-specific context is very limited. Also, different output between multiple experiment platforms may introduce extra complexity in analyzing the molecular function of these variants. We developed GRAM, a generalized model to predict molecular effect of non-coding variants in multiple cell types for different experimental platforms. We first selected the most informative cell-independent SELEX transcription factor binding score on the variant locus as features and then combine cell-specific gene expression profile to build a multi-step prediction model. GRAM has been successfully tested on both MPRA and Luciferase assay, and on three different cell lines: GM12878, K562 and MCF7, shows high performance.

bioinformatics↗

bioRxiv2018

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs

Fusion transcripts are used as biomarkers in companion diagnoses. Although more than 15,000 fusion RNAs have been identified from diverse cancer types, few common feature has been reported. Here, we compared 16,410 fusion transcripts detected in cancer (from a published cohort of 9,966 tumor samples of 33 cancer types) with genome-wide RNA-DNA interactions mapped in two normal, non-cancerous cell types (using iMARGI, an enhanced version of the MARGI [Mapping RNA-Genome Interactions assay]). Among the top 10 most significant RNA-DNA interactions in normal cells, 5 co-localized with the gene pairs that formed fusion RNAs in cancer. Furthermore, throughout the genome, the frequency of a gene pair to exhibit RNA-DNA interactions is positively correlated with the probability of this gene pair to present documented fusion transcripts in cancer. To test whether RNA-DNA interactions in normal cells are predictive of fusion RNAs, we analyzed in a validation cohort of 96 lung cancer samples using RNA-seq. We found 34 out of 42 fusion transcripts in the validation cohort exhibited RNA-DNA interactions in normal cells. Finally, combining RNA-seq, single-molecule RNA FISH, and DNA FISH, we detected a cancer sample with Eml4-Alk fusion RNA without forming the Eml4-Alk fusion gene. Collectively, these data suggest a novel RNA-poise model, where spatial proximity of RNA and DNA could poise for creation of fusion transcripts.

systems biology↗

bioRxiv2018

Distance-based Protein Folding Powered by Deep Learning

Direct coupling analysis (DCA) for protein folding has made very good progress, but it is not effective for proteins that lack many sequence homologs, even coupled with time-consuming folding simulation. We show that we can accurately predict the distance matrix of a protein by deep learning, even for proteins with [~]60 sequence homologs. Using only the geometric constraints given by the resulting distance matrix we may construct 3D models without involving any folding simulation. Our method successfully folded 21 of the 37 CASP12 hard targets with a median family size of 58 effective sequence homologs within 4 hours on a Linux computer of 20 CPUs. In contrast, DCA cannot fold any of these hard targets in the absence of folding simulation, and the best CASP12 group folded only 11 of them by integrating DCA-predicted contacts into complex, fragment-based folding simulation. Rigorous experimental validation in CASP13 shows that our distance-based folding server successfully folded 17 of 32 hard targets (with a median family size of 36 sequence homologs) and obtained 70% precision on top L/5 long-range predicted contacts. Latest experimental validation in CAMEO shows that our server predicted correct fold for two membrane proteins of new fold while all the other servers failed. These results imply that it is now feasible to predict correct fold for proteins lack of similar structures in PDB on a personal computer without folding simulation.\n\nSignificanceAccurate description of protein structure and function is a fundamental step towards understanding biological life and highly relevant in the development of therapeutics. Although greatly improved, experimental protein structure determination is still low-throughput and costly, especially for membrane proteins. As such, computational structure prediction is often resorted. Predicting the structure of a protein with a new fold (i.e., without similar structures in PDB) is very challenging and usually needs a large amount of computing power. This paper shows that by using a powerful deep learning technique, even with only a personal computer we can predict new folds much more accurately than ever before. This method also works well on membrane protein folding.

bioinformatics↗

bioRxiv2018

Wolbachia pipientis occurs in Aedes aegypti populations in New Mexico and Florida, USA

The mosquitoes Aedes aegypti (L.) and Ae. albopictus Skuse are the major vectors of dengue, Zika, yellow fever and chikungunya viruses worldwide. Wolbachia, an endosymbiotic bacterium present in many insects, is being utilized in novel vector control strategies to manipulate mosquito life history and vector competence to curb virus transmission. Earlier studies have found that Wolbachia is commonly detected in Ae. albopictus but sporadically detected in Ae. aegypti. In this study, we used a two-step PCR assay to detect Wolbachia in wild-collected samples of Ae. aegypti. The PCR products were sequenced to validate amplicons and identify Wolbachia strains. A Loop-mediated isothermal amplification (LAMP) assay was developed and used for detecting Wolbachia in selected mosquito specimens as well. We found Wolbachia in 85/148 (57.4%) wild specimens of Ae. aegypti from various cities in New Mexico and in 2/46 (4.3%) wild specimens of Ae. aegypti from St. Augustine, Florida. We did not detect Wolbachia in 94 samples of Ae. aegypti from Deer Park, Harris County, Texas. Wolbachia detected in Ae. aegypti from both New Mexico and Florida was the wAlbB strain of Wolbachia pipientis. A Wolbachia positive colony of Ae. aegypti was established from pupae collected in Las Cruces, New Mexico in 2018.

ecology↗

bioRxiv2018

Atlas of Subcellular RNA Localization Revealed by APEX-seq

We introduce APEX-seq, a method for RNA sequencing based on spatial proximity to the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome, revealing extensive and exquisite patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.

cell biology↗

bioRxiv2018

Brg1 controls neurosensory cell fate commitment and differentiation in the mammalian inner ear

Otic ectoderm gives rise to almost all cell types of the inner ear; however, the mechanisms that link transcription factors, chromatin, lineage commitment and differentiation capacity are largely unknown. Here we show that Brg1 chromatin-remodeling factor is required for specifying neurosensory lineage in the otocyst and for inducing hair and supporting cell fates in the cochlear sensory epithelium. Brg1 interacts with the critical neurosensory-specific transcription factors Eya1/Six1, both of which simultaneously interact with BAF60a or BAF60c. Chromatin immunoprecipitation-sequencing (ChIP-seq) and ChIP assays demonstrate Brg1 association with discrete regulatory elements at the Eya1 and Six1 loci. Brg1-deficiency leads to markedly decreased Brg1 binding at these elements and loss of Eya1 and Six1 expression. Furthermore, ChIP-seq reveals Brg1-bound promoter-proximal and distal regions near genes essential for inner ear morphogenesis and cochlear sensory epithelium development. These findings uncover essential functions for chromatin-remodeling in the activation of neurosensory fates during inner ear development.

developmental biology↗