Ping Li

Ping Li
Beijing Institute of Biotechnology, Beijing, China

PhD

About

33
Publications
2,831
Reads
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177
Citations
Citations since 2017
15 Research Items
167 Citations
20172018201920202021202220230102030
20172018201920202021202220230102030
20172018201920202021202220230102030
20172018201920202021202220230102030
Additional affiliations
June 2017 - present
Beijing Institute of Biotechnology
Position
  • Research Assistant
Education
September 2012 - June 2017
Beijing Institute of Biotechnology
Field of study
September 2008 - June 2012
Shandong University
Field of study

Publications

Publications (33)
Article
Full-text available
Mitosis entails global and dramatic alterations, such as higher‐order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re‐establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription f...
Article
Full-text available
Vaccines are a key weapon against the COVID-19 pandemic caused by SARS-CoV-2. However, there are inter-individual differences in immune response to SARS-CoV-2 vaccines and genetic contributions to these differences have barely been investigated. Here, we performed genome-wide association study (GWAS) of antibody levels in 168 inactivated SARS-CoV-2...
Article
Full-text available
The COVID-19 pandemic has resulted in great morbidity and mortality worldwide and human genetic factors have been implicated in the susceptibility and severity of COVID-19. However, few replicate researches have been performed, and studies on associated genes mainly focused on genic regions while regulatory regions were a lack of in-depth dissectio...
Article
Full-text available
RNA species act as architectural scaffolds for nuclear structures including chromatin in eukaryotic cells. However, the composition and dynamics of tightly bound chromatin associated RNAs during mitosis remains elusive. Here we report the identification of chromatin enriched RNA (cheRNAs) by biochemical nuclear fractionation coupled with RNA-seq in...
Article
Full-text available
Background Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 plays as a transcriptional activator that promotes hepatocellular cancer (HCC) cell proliferation and cell cycle transition. However,...
Article
Full-text available
Human genetics has been proposed to play an essential role in inter-individual differences in respiratory virus infection occurrence and outcomes. To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and...
Preprint
Full-text available
Human genetics has been proposed to play an essential role in inter-individual differences in respiratory virus infection occurrence and outcomes. To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and...
Article
Full-text available
The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5′-UTR and 3′-UTR, frameshifting element (FSE) pseudokno...
Preprint
Full-text available
The SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3'-UTR and 5'-UTR, framesh...
Article
Full-text available
The growth rate of bacteria increases under simulated microgravity (SMG) with low-shear force. The next-generation microbial chassis Vibrio natriegens (V. natriegens) is a fast-growing Gram-negative, non-pathogenic bacterium with a generation time of less than 10 min. Screening of a V. natriegens strain with faster growth rate was attempted by 2-we...
Article
Long-term observation of transcriptome dynamics of COVID-19 patients is urgently needed. In this report, we performed the longitudinal peripheral blood transcriptome profiling after diagnosis in five patients, and found that patients' blood transcriptomes undergo dramatic and consistent changes in early recovery stage (ERS). Meanwhile, the blood tr...
Article
The interphase chromatin is folded in the nucleus in a hierarchical manner, including the nucleosome, the "beads on a string" structure composed of nucleosomes, the solenoid fiber structure, the chromatin/DNA loop structure (chromatin/DNA loop), and the topologically associated domain (TAD). Among them, TAD is considered to be the basic unit of the...
Article
Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C exper...
Article
Interferon-induced transmembrane protein (IFITM) 1, 2 and 3 are a family of interferon (IFN)-induced transmembrane proteins that block entry of a broad spectrum of pathogens. However, the transcriptional regulation of these genes, especially whether there exists any enhancers and their roles during the IFN induction process remain elusive. Here, co...
Article
Full-text available
Circadian rhythm exerts its influence on animal physiology and behavior by regulating gene expression at various levels. Here we systematically explored circadian long non-coding RNAs (lncRNAs) in mouse liver and examined their circadian regulation. We found that a significant proportion of circadian lncRNAs are expressed at enhancer regions, mostl...
Preprint
Background The spatial organization of interphase chromatin in the nucleus play an important role in gene expression regulation and function. With the rapid development of revolutionized chromosome conformation capture technology and its genome-wide derivatives such as Hi-C, investigation of the genome folding becomes more efficient and convenient....
Article
Full-text available
Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes in vivo. As genome-wide transcription is organized under the high-order chromosome structure, it is largely uncharted how circadian gene expression is influenced by chro...
Data
(a) The Bmal1-bound circadian enhancer upstream 8 kb of Nr1d1. The genome browser shows the binding profiles of H3K4me1, H3K27ac, Bmal1 (in liver and MEFs), Nr1d1, cohesin, and CTCF around the 4C bait. Bmal1 ChIP-Seq in MEFs was conducted in this study and other ChIP-Seq data showed in here were re-analyzed from published data (Methods). (b) The Bm...
Data
Ninety-seven Bmal1super-enhancers in mouse liver ranked by Bmal1 signal. (XLSX)
Data
Bmal1 regulatory potentials in cohesin/CTCF dependent model and background model. The 3rd and 4th columns show the regulatory potentials when we only incorporate cohesin-non-CTCF or cohesin-CTCF effect in background model. The JTK_cycle q value and circadian phases of genes in mouse liver are showed in 6th and 7th column respectively. In this study...
Data
All primers used in this study. (XLSX)
Data
Peak calling results for Bmal1 ChIP-Seq in MEF cells and DESeq results for RNA-Seq in control and Smc3-/- MEFs. (XLSX)
Data
The read profiles of 4C samples in the upstream and downstream 2 Mb region to the bait. The highly interacting region (150 kb to the bait) is indicated by the region between two red lines. The Hi-C data in mouse embryonic stem cells [12] showed that highly interacting region of the enhancer is restricted in a topologically associating domain (black...
Data
(a) The distributions of Nr1d1 regulatory potentials for COGs and non-COGs in background model and cohesin/CTCF dependent model. The COGs in cohesin/CTCF dependent model as well as in the model with only cohesin-CTCF or cohesin-non-CTCF effect have significantly higher potentials than in background model (KS test, p = 10−16). (b) The distribution o...
Data
(a) The genome browser shows the binding profiles of cohesin, Nr1d1, H3K4me1, H3K27ac, cohesin loop around Ahnak, and RNA-Seq profile in Smc3-/- MEFs. The locations of the 3C primers for enhancer-promoter interaction analysis were indicated. Two Nr1d1 binding sites (marked by asterisk) are located downstream 106 kb and 108 kb of Ahnak respectively....
Data
(a) The Bmal1 ChIP-qPCR signal relative to input on the enhancer of Phldb2 in mouse liver (compared to IgG ChIP t-test p = 0.001, mean+/-SD, 2 biological replicates, 2 technical replicates). (b) CRISPR-CAS9 deletion of the cohesin binding site near the enhancer of Phldb2 in Hepa1-6 cells. Gel electrophoresis shows the homologous arms (Homology), co...
Data
Enhancer interacting regions at CT6 and CT18. (XLSX)
Data
(a) The circadian index around protein binding sites defined from the transcription of positive strand in GRO-Seq (GSE59486, Methods). The result from negative strand was showed in Fig 3A. (b) The circadian index around protein binding sites defined from the transcription in RNA-Seq (GSE39860, Methods). (c) A depiction of our procedure to calculate...
Data
The statistics of sequencing reads of 4C-Seq, ChIP-Seq, and RNA-Seq conducted in this study. (XLSX)
Article
ZNF143 is a ubiquitously expressed transcription factor conserved in vertebrates and might regulate the expression of numerous genes. But its function in mediating chromatin interactions remains elusive. By integrated analysis of public datasets, we provided evidence that a majority of ZNF143 binding sites (BSs) were involved in CTCF-mediated chrom...
Article
Full-text available
ZNF143 is a ubiquitously expressed transcription factor conserved in vertebrates and might regulate the expression of numerous genes. But its function in mediating chromatin interactions remains elusive. By integrated analysis of public datasets, we provided evidence that a majority of ZNF143 binding sites (BSs) were involved in CTCF-mediated chrom...
Article
Full-text available
Anthrax toxin causes anthrax pathogenesis and expression levels of ANTXR2 (anthrax toxin receptor 2) are strongly correlated with anthrax toxin susceptibility. Previous studies found that ANTXR2 transcript abundance varies considerably in individuals of different ethnic/geographical groups, but no eQTLs (expression quantitative trait loci) have bee...
Article
Accumulating evidence indicates that some miRNAs could form feedback loops with their targets to fine-tune tissue homeostasis, while disruption of these loops constitutes an essential step towards human tumorigenesis. In this study, we report the identification of a novel negative feedback loop formed between miR-139 and its oncogenic target Jun. I...

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