Biology subjects

Cui, K.

Publications and source records attributed to Cui, K..

26 records · Page 2Linked to original sources

bioRxiv2022

Hi-TrAC reveals fine-scale chromatin structures organized by transcription factors

The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to understand the temporospatial regulation of gene expression. In this study, we report Hi-TrAC as a proximity ligation free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among accessible regulatory elements. Hi-TrAC detects chromatin looping among accessible chromatin regions at single nucleosome resolution. With almost half-million identified loops, we constructed a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors, we discovered that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, related to domain formation; whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression. Thus, we developed a new methodology to identify a delicate and comprehensive network of cis-regulatory elements, revealing the complexity and a division of labor of TFs in chromatin looping for genome organization and gene expression.

genomics↗

bioRxiv2021

ProDCoNN-server: a web server for protein sequence prediction and design from a three-dimensional structure

We present ProDCoNN-server, a web server for protein sequence design and prediction from a given protein structure. The server is based on a previously developed deep learning model for protein design, ProDCoNN, which achieved state-of-the-art performance when tested on large numbers of test proteins and benchmark datasets. The prediction is very fast compared with other protein sequence prediction servers - it takes only a few minutes for a query protein on average. Two models could be selected for different purposes: BBO for full sequence prediction, extendable for multiple sequence generation, and BBS for single position prediction with the type of other residues known. ProDCoNN-server outputs the predicted sequence and the probability matrix for each amino acid at each predicted residue. The probability matrix can also be visualized as a sequence logos figure (BBO) or probability distribution plot (BBS). The server is available at: https://prodconn.stat.fsu.edu/.

bioinformatics↗

bioRxiv2021

High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions

Fasciola gigantica and Fasciola hepatica are causative pathogens of fascioliasis, with the widest latitudinal, longitudinal, and altitudinal distribution; however, among parasites, they have the largest sequenced genomes, hindering genomic research. In the present study, we used various sequencing and assembly technologies to generate a new high-quality Fasciola gigantica reference genome. We improved the integration of gene structure prediction, and identified two independent transposable element expansion events contributing to (1) the speciation between Fasciola and Fasciolopsis during the Cretaceous-Paleogene boundary mass extinction, and (2) the habitat switch to the liver during the Paleocene-Eocene Thermal Maximum, accompanied by gene length increment. Long interspersed element (LINE) duplication contributed to the second transposon-mediated alteration, showing an obvious trend of insertion into gene regions, regardless of strong purifying selection. Gene ontology analysis of genes with long LINE insertions identified membrane-associated and vesicle secretion process proteins, further implicating the functional alteration of the gene network. We identified 852 excretory/secretory proteins and 3300 protein-protein interactions between Fasciola gigantica and its host. Among them, copper/zinc superoxide dismutase genes, with specific gene copy number variations, might play a central role in the phase I detoxification process. Analysis of 559 single-copy orthologs suggested that Fasciola gigantica and Fasciola hepatica diverged at 11.8 Ma near the Middle and Late Miocene Epoch boundary. We identified 98 rapidly evolving gene families, including actin and aquaporin, which might explain the large body size and the parasitic adaptive character resulting in these liver flukes becoming epidemic in tropical and subtropical regions.

genomics↗

bioRxiv2020

Modeling SARS-CoV-2 infection in vitro with a human intestine-on-chip device

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) has given rise to a global pandemic. The gastrointestinal symptoms of some COVID-19 patients are underestimated. There is an urgent need to develop physiologically relevant model that can accurately reflect human response to viral infection. Here, we report the creation of a biomimetic human intestine infection model on a chip system that allows to recapitulate the intestinal injury and immune response induced by SARS-CoV-2, for the first time. The microengineered intestine-on-chip device contains human intestinal epithelium (co-cultured human intestinal epithelial Caco-2 cells and mucin secreting HT-29 cells) lined in upper channel and vascular endothelium (human umbilical vein endothelial cells, HUVECs) in a parallel lower channel under fluidic flow condition, sandwiched by a porous PDMS membrane coated with extracellular matrix (ECM). At day 3 post-infection of SARS-CoV-2, the intestine epithelium showed high susceptibility to viral infection and obvious morphological changes with destruction of intestinal villus, dispersed distribution of mucus secreting cells and reduced expression of tight junction (E-cadherin), indicating the destruction of mucous layer and the integrity of intestinal barrier caused by virus. Moreover, the endothelium exhibited abnormal cell morphology with disrupted expression of adherent junction protein (VE-cadherin). Transcriptional analysis revealed the abnormal RNA and protein metabolism, as well as activated immune responses in both epithelial and endothelial cells after viral infection (e.g., up-regulated cytokine genes, TNF signaling and NF-kappa B signaling-related genes). This bioengineered in vitro model system can mirror the human relevant pathophysiology and response to viral infection at the organ level, which is not possible in existing in vitro culture systems. It may provide a promising tool to accelerate our understanding of COVID-19 and devising novel therapies.

bioengineering↗

bioRxiv2020

A human disease model of SARS-CoV-2-induced lung injury and immune responses with a microengineered organ chip

Coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that seriously endangers human health. There is an urgent need to build physiological relevant human models for deep understanding the complex organ-level disease processes and facilitating effective therapeutics for COVID-19. Here, we first report the use of microengineered alveolus chip to create a human disease model of lung injury and immune responses induced by native SARS-CoV-2 at organ-level. This biomimetic system is able to reconstitute the key features of human alveolar-capillary barrier by co-culture of alveolar epithelial and microvascular endothelial cells under microfluidic flow. The epithelial cells on chip showed higher susceptibility to SARS-CoV-2 infection than endothelial cells identified by viral spike protein expression. Transcriptional analysis showed distinct responses of two cell types to SARS-CoV-2 infection, including activated type I interferon (IFN-I) signaling pathway in epithelium and activated JAK-STAT signaling pathway in endothelium. Notably, in the presence of circulating immune cells, a series of alveolar pathological changes were observed, including the detachment of endothelial cells, recruitment of immune cells, and increased production of inflammatory cytokines (IL-6, IL-8, IL-1{beta} and TNF-). These new findings revealed a crucial role of immune cells in mediating lung injury and exacerbated inflammation. Treatment with antiviral compound remdesivir could suppress viral copy and alleviate the disruption of alveolar barrier integrity induced by viral infection. This bioengineered human organ chip system can closely mirror human-relevant lung pathogenesis and immune responses to SARS-CoV-2 infection, not possible by other in vitro models, which provides a promising and alternative platform for COVID-19 research and preclinical trials.

bioengineering↗

bioRxiv2019

Genomic features of BRDT binding sites in gene units suggest transcriptional partners and specific epigenetic landscapes to regulate transcriptional activity during spermatogenesis

BRDT, a member of the BET family of double bromodomain-containing proteins, is expressed uniquely in the male germ line, is essential for spermatogenesis in the mouse, and binds to acetylated transcription start sites of genes expressed in meiosis and spermiogenesis. It has thus been postulated to be a key regulator of transcription in meiotic and post-meiotic cells. To understand the function of BRDT in regulating gene expression, we characterized its genome-wide distribution, in particular the features of the BRDT binding sites within gene units, by ChIP-Seq analysis of enriched fractions of spermatocytes and spermatids. In both cell types, BRDT binding sites were mainly located in promoters, first exon, and introns of genes that are highly transcribed during meiosis and spermiogenesis. Furthermore, in promoters, BRDT binding sites overlapped with several histone modifications and histone variants associated with active transcription, and were also enriched for consensus sequences for specific transcription factors, including MYB, RFX, ETS and ELF1 in pachytene spermatocytes, and JunD, c-Jun, CRE and RFX in round spermatids. Our analysis further revealed that BRDT-bound genes play key roles in diverse biological processes that are essential for proper spermatogenesis. Taken together, our data suggest that BRDT is involved in the recruitment of different transcription factors to distinctive chromatin regions within gene units to regulate diverse downstream target genes that function in male meiosis and spermiogenesis.

developmental biology↗

bioRxiv2019

Principles of 3D Nucleus Organization and Epigenetic Regulation in Diploid Genome Revealed by Multi-omic Data from Hybrid Mouse

Most mammalian genomes are diploid and previous studies have extensively investigated the average epigenetic profiles of homologous chromosomes. Here we use hybrid mice to distinguish the epigenetic status and three-dimensional organization of homologous chromosomes. We generated Hi-C, ChIP-seq and RNA-seq datasets from CD4 T cells of B6, Cast and hybrid mice, respectively, and systematically analyzed the 3D nucleus organization and epigenetic regulation. Our data indicate that the inter-chromosomal interaction patterns between homologous chromosomes are similar and the similarity is highly correlated with their allelic co-expression levels. Construction of 3D nucleus based on allele-specific interaction frequency revealed symmetric positioning of homologous chromosomes in the 3D nuclear space. The inter-chromosomal interactions at centromeres are significantly weaker than those at telomeres, indicating positioning of centromeres toward the inside of chromosome territories and telomeres toward the surface of chromosome territories. The majority A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments due to cis-effect. About 95% of the trans-effected B6/Cast divergent compartments converge to same compartment status potentially due to a shared cellular environment. We found the differentially expressed genes between the two haploids in hybrid were associated with either genetic associated cis-effects or epigenetic associated trans-effects. The widespread epigenetic differences between B6 and Cast suggest that epigenetic changes may be major contributors to differences between B6 and Cast. Our data revealed symmetrical positioning of homologous chromosomes in 3D nucleus and enhanced our understanding of allele-specific epigenetic regulation.

genomics↗

bioRxiv2019

Crl activates transcription by stabilizing the active conformation of the master stress factor σS

{sigma}S is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses and antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of {sigma}S-mediated transcription requires a {sigma}S-specific activator, Crl. In this study, we determined a 3.80 [A] cryo-EM structure of an E. coli transcription activation complex (E. coli Crl-TAC) comprising E. coli {sigma}S-RNAP holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with the domain 2 of {sigma}S ({sigma}S2), sharing no interaction with promoter DNA. Subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) results indicate that Crl stabilizes key structural motifs of {sigma}S2 to promote the assembly of {sigma}S-RNAP holoenzyme and also to facilitate formation of the RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.

biochemistry↗