Biology subjects

Yong Chen

Publications and source records attributed to Yong Chen.

3 recordsLinked to original sources

bioRxiv2020

Molecular architecture of the SARS-CoV-2 virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins and the complexes of the spike (S) proteins with the cellular receptor ACE2 or neutralizing antibodies, detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in both pre- and postfusion conformations were determined to average resolutions of 8.7-11 [A]. Compositions of the N-linked glycans from the native spikes were analyzed by mass-spectrometry, which revealed highly similar overall processing states of the native glycans to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNP) and its higher-order assemblies were revealed. Overall, these characterizations have revealed the architecture of the SARS-CoV-2 virus in unprecedented detail, and shed lights on how the virus packs its [~]30 kb long single-segmented RNA in the [~]80 nm diameter lumen.

microbiology↗

bioRxiv2016

RSQ: a statistical method for quantification of isoform-specific structurome using transcriptome-wide structural profiling data

The structure of RNA, which is considered to be a second layer of information alongside the genetic code, provides fundamental insights into the cellular function of both coding and non-coding RNAs. Several high-throughput technologies have been developed to profile transcriptome-wide RNA structures, i.e., the structurome. However, it is challenging to interpret the profiling data because the observed data represent an average over different RNA conformations and isoforms with different abundance. To address this challenge, we developed an RNA structurome quantification method (RSQ) to statistically model the distribution of reads over both isoforms and RNA conformations, and thus provide accurate quantification of the isoform-specific structurome. The quantified RNA structurome enables the comparison of isoform-specific conformations between different conditions, the exploration of RNA conformation variation affected by single nucleotide polymorphism (SNP),and the measurement of RNA accessibility for binding of either small RNAs in RNAi-based assays or RNA binding protein in transcriptional regulation. The model used in our method sheds new light on the potential impact of the RNA structurome on gene regulation.

Bioinformatics↗

bioRxiv2016

Droplets bumpers as mechanical sensors for cell migration under confinement

Mechanical cell forces play determinant roles in cell growth and tissue development. Cell migration is a relevant context to explore single cell forces, since mechanotransduction and cell morphology are dynamically and biochemically co-regulated in order to modulate cell shape changes minute to minute. In this work we present the design of a hybrid microdevice made from a set of parallel PDMS microchannels in which oil emulsion droplets are introduced to be used as biocompatible and deformable cell forces transducers upon HL-60 human leukemia cell line migration. We show that the mechanical stress exerted by the cells can be measured from the analysis of the droplets deformations at the single cell level. Finally we show that acto-myosin contraction plays a role in the cell ability to cross obstacles in confinement conditions.

Cell Biology↗