Biology subjects

Bing, X.

Publications and source records attributed to Bing, X..

6 recordsLinked to original sources

bioRxiv2023

Chromosome Structure I: Loop extrusion or boundary:boundary pairing?

Two different models have been proposed to explain how the endpoints of chromatin looped domains ("TADs") in eukaryotic chromosomes are determined. In the first, a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop. In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of MicroC to analyze how TADs are organized, and experimental manipulations of the even skipped TAD boundary, homie, to test the predictions of the "loop-extrusion" and the "boundary-pairing" models. Our findings are incompatible with the loop-extrusion model and instead suggest that the endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their partners, either head-to-head or head-to-tail, with varying degrees of specificity. Although our experiments do not address how partners find each other, the mechanism is unlikely to require loop extrusion.

genetics↗

bioRxiv2022

SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains

Modern multi-omic technologies can generate deep multi-scale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make the analyses and integration of high-dimensional omic datasets challenging. Here, we present Significant Latent factor Interaction Discovery and Exploration (SLIDE), a first-in-class interpretable machine learning technique for identifying significant interacting latent factors underlying outcomes of interest from high-dimensional omic datasets. SLIDE makes no assumptions regarding data-generating mechanisms, comes with theoretical guarantees regarding identifiability of the latent factors/corresponding inference, outperforms/performs at least as well as state-of-the-art approaches in terms of prediction, and provides inference beyond prediction. Using SLIDE on scRNA-seq data from systemic sclerosis (SSc) patients, we first uncovered significant interacting latent factors underlying SSc pathogenesis. In addition to accurately predicting SSc severity and outperforming existing benchmarks, SLIDE uncovered significant factors that included well-elucidated altered transcriptomic states in myeloid cells and fibroblasts, an intriguing keratinocyte-centric signature validated by protein staining, and a novel mechanism involving altered HLA signaling in myeloid cells, that has support in genetic data. SLIDE also worked well on spatial transcriptomic data and was able to accurately identify significant interacting latent factors underlying immune cell partitioning by 3D location within lymph nodes. Finally, SLIDE leveraged paired scRNA-seq and TCR-seq data to elucidate latent factors underlying extents of clonal expansion of CD4 T cells in a nonobese diabetic model of T1D. The latent factors uncovered by SLIDE included well-known activation markers, inhibitory receptors and intracellular regulators of receptor signaling, but also honed in on several novel naive and memory states that standard analyses missed. Overall, SLIDE is a versatile engine for biological discovery from modern multi-omic datasets.

systems biology↗

bioRxiv2021

CausER - a framework for inferring causal latent factors using multi-omic human datasets

High-dimensional cellular and molecular profiling of human samples highlights the need for analytical approaches that can integrate multi-omic datasets to generate predictive biomarkers and prioritized causal inferences. Current methods are limited by high dimensionality of the combined datasets, the differences in their data distributions and their integration to infer causal relationships. Here we present Essential Regression (ER), an interpretable machine learning approach for high-dimensional multi-omic datasets, that addresses these problems by identifying latent factors and their likely cause-effect relationships with the system-wide outcome/properties of interest. ER is a novel data-distribution-free latent-factor regression model that integrates multi-omic datasets and identifies latent factors significantly associated with an outcome. ER outperforms a range of state-of-the-art methods in terms of prediction performance on simulated datasets. ER can be coupled with probabilistic graphical modeling thereby strengthening the causal inferences. ER generates novel cellular and molecular predictions, using multi-omic human systems immunology datasets, pertaining to immunosenescence and immune dysregulation.

systems biology↗

bioRxiv2018

Zebrafish DANA retroposon can form large zebrafish sequence in human Hepg2 and 293T cell lines

In this study, we cloned small zebrafish retroposon DANA from zebrafish genome and constructed the lentiviral expression vector pEB-GFP (T2A)PURO. Three human cell lines including 293T, Hepg2 and LO2 were selected as infection targets. After detecting the expression of DANA, we found that the expression of DANA retroposon in three cells had different effects on cell lines through chromosome walking. Among these cells, LO2 showed no DANA retrotrans-position, while 293T and Hepg2 cell lines displayed retrotrans-position with the formation of some zebrafish genome fragments. Thereafter, we constructed a mutant of DANA retroposon and infected it in 293T cells, but no retrotrans-position was found after chromosome walking. Re-sequencing of the two cell lines (293T and Hepg2) showed that a large number of zebrafish genome fragments were found in the genomes of both cell lines, which could be divided into four types. The first type was zebrafish microsatellite sequence, accounting for 79.23% and 74.45% in 293T cell line and Hepg2 cell line, respectively. The second type was the sequence with a small amount of poly A or T, and the third type was the sequence with poly G or C, and the second and third types accounted very low proportion. The fourth type was composed of coding sequence and non-coding sequence, with large difference and very low proportion of common sequences between the two cell lines. Taken together, this study indicated that zebrafish DANA retroposon can result in retrotrans-position using the retrotrans system of human cell lines.

cell biology↗

bioRxiv2018

Rearranged zebrafish genomic DNA induces zebrafish mutant after microinjection into fertilized egg and preliminary study of the mechanism

Genomic DNA of zebrafish was first digested incompletely with Msp I, and then the fragments were joined to form rearranged genomic DNA. This rearranged genomic DNA was incompletely digested with EcoR I, and the fragments were linked with a long adaptor. Two primers (Gmprimer1 and Gmprimer2) were designed according to the adaptor sequence for two-step amplification. The Gmprimer1-amplified products were microinjected into fertilized zebrafish eggs after purification and a red flesh mutant was observed among 42 surviving zebrafish. We obtained several introduced sequences by two-step amplification. The second set of Gmprimer2-amplified products were purified and microinjected into fertilized zebrafish eggs; all 37 surviving fish were red flesh mutants. We found that the largest amplified band from the mutant from the first microinjection was also present in the amplified pattern from six mutants from the second microinjection. The length of the sequence was 2,565 bp, but it did not encode any proteins. Microinjecting this sequence into fertilized zebrafish eggs produced the red flesh mutant. The sequences differed slightly among different individuals from the second microinjection. Most regions of these sequences were the same, with the exception of a hypervariable region. We mixed 10 such sequences equally and microinjected them into zebrafish zygotes; the findings showed that most zygotes died and the surviving zebrafish were almost all mutants. By genome walking, we found that the site of insertion of the fragment was the same, beginning at position 41,365,003 of the eighth chromosome, and that downstream of the introduced fragment is a conservative sequence of 6,536 bp (named Cao-sequence), starting from a small reverse repeat sequence, not encoding any gene, nor similar to any known regulatory sequence. It has 322 homologous sequences in the zebrafish genome, which are distributed in all chromosomes. We designed two primers within Cao-sequence and several primers specific for different locations upstream of it. Compared with normal zebrafish, we found that the amplified patterns of all mutants in Cao-sequence regions changed to varying degrees. To further understand the effect of the introduced sequence on the zebrafish genomes, we selected six mutants for whole-genome resequencing. The results showed that numerous Cao-sequences from these six mutants were partially deleted and the lengths of the deletions was mostly approximately 6,100 bp, being located at the 5' end of Cao-sequences. Among them, 43 Cao-sequence loci were commonly deleted from the six mutants (with slightly different locations), and the other deletion sites were not identical. We think that different deletion combinations of Cao-sequence may show different mutation characteristics. The tail part from four red flesh mutants and three individuals of wild type were collected for transcriptome sequencing. TopGO analysis showed that the 4 most significant enrichment nodes were sequence specific DNA binding proteins, sequence specific transcription factors, chromatin proteins and zinc binding proteins. The results of KEGG enrichment analysis showed that the top four affected KEGG-pathways were metabolic pathways, oxidative phosphorylation, citrate cycle and 2-oxocarboxylic acid metabolism.We conclude that deletion of Cao-sequence can affect the expression of a series of transcription regulators and specific DNA binding proteins, then many basic metabolic processes were disturbed which led to mutations.

genetics↗

bioRxiv2017

A fine-tuned vector-parasite dialogue in tsetse’s cardia determines peritrophic matrix integrity and trypanosome transmission success

Arthropod vectors have multiple physical and immunological barriers that impede the development and transmission of parasites to new vertebrate hosts. These barriers include the peritrophic matrix (PM), a chitinous barrier that separates the blood bolus from the midgut epithelia and inturn, modulates vector-microbiota interactions. In tsetse flies, a sleeve-like PM is continuously produced by the cardia organ located at the fore- and midgut junction. African trypanosomes, Trypanosoma brucei, must bypass the PM twice; first to colonize the midgut and secondly to reach the salivary glands (SG), to complete their transmission cycle in tsetse. However, not all flies with midgut infections develop mammalian transmissible SG infections - the reasons for which are unclear. Here, we used transcriptomics, microscopy and functional genomics analyses to understand the factors that regulate parasite migration from midgut to SG. In flies with midgut infections only, parasites fail to cross the PM as they are eliminated from the cardia by reactive oxygen intermediates (ROIs) - albeit at the expense of collateral cytotoxic damage to the cardia. In flies with midgut and SG infections, expression of genes encoding components of the PM is reduced in the cardia, and structural integrity of the PM barrier is compromised. Under these circumstances trypanosomes traverse through the newly secreted and compromised PM. The process of PM attrition that enables the parasites to re-enter into the midgut lumen is apparently mediated by components of the parasites residing in the cardia. Thus, a fine-tuned dialogue between tsetse and trypanosomes at the cardia determines the outcome of PM integrity and trypanosome transmission success.\n\nAuthor summaryInsects are responsible for transmission of parasites that cause deadly diseases in humans and animals. Understanding the key factors that enhance or interfere with parasite transmission processes can result in new control strategies. Here, we report that a proportion of tsetse flies with African trypanosome infections in their midgut can prevent parasites from migrating to the salivary glands, albeit at the expense of collateral damage. In a subset of flies with gut infections, the parasites manipulate the integrity of a midgut barrier, called the peritrophic matrix, and reach the salivary glands for transmission to the next mammal. Either targeting parasite manipulative processes or enhancing peritrophic matrix integrity could reduce parasite transmission.

microbiology↗