A5100416506- RNA Research and Splicing
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- RNA and protein synthesis mechanisms
- Protein Degradation and Inhibitors
- Cancer, Lipids, and Metabolism
- Protein Structure and Dynamics
- Cancer-related molecular mechanisms research
- Lipid metabolism and biosynthesis
- Genomics and Chromatin Dynamics
- DNA and Nucleic Acid Chemistry
- Heat shock proteins research
- Nuclear Structure and Function
- Epigenetics and DNA Methylation
- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Renal and related cancers
- MicroRNA in disease regulation
- Autophagy in Disease and Therapy
- Tryptophan and brain disorders
- Bioinformatics and Genomic Networks
- Inorganic Chemistry and Materials
- Metalloenzymes and iron-sulfur proteins
- Animal Genetics and Reproduction
- Plant Molecular Biology Research
Peking University
2016-2025
National Health and Family Planning Commission
2022-2025
Institute of Genetics and Developmental Biology
2025
Chinese Academy of Sciences
2004-2025
Peking University Sixth Hospital
2024-2025
National Center of Biomedical Analysis
2021-2025
Center for Life Sciences
2024
South China Agricultural University
2024
Chinese Institute for Brain Research
2024
National Clinical Research Center for Digestive Diseases
2024
Abstract Background Though most of the transcripts are long non-coding RNAs (lncRNAs), little is known about their functions. lncRNAs usually function through interactions with proteins, which implies importance identifying binding proteins in understanding molecular mechanisms underlying functions lncRNAs. Only a few approaches available for predicting between and proteins. In this study, we introduce new method lncPro. Results By encoding RNA protein sequences into numeric vectors, used...
Abstract It's widely appreciated that liquid–liquid phase separation (LLPS) underlies the formation of membraneless organelles, which function to concentrate proteins and nucleic acids. In past few decades, major efforts have been devoted identify associated elucidate their functions. To better utilize knowledge dispersed in published literature, we developed PhaSepDB (http://db.phasep.pro/), a manually curated database proteins. Currently, includes 2914 non-redundant localized different...
Protein self-assembly is one of the formation mechanisms biomolecular condensates. However, most phase-separating systems (PS) demand multiple partners in biological conditions. In this study, we divided PS proteins into two groups according to mechanism by which they undergo PS: PS-Self can self-assemble spontaneously form droplets, while PS-Part interact with PS. Analysis amino acid composition revealed differences sequence pattern between protein groups. Existing predictors, when...
Abstract Lack of detailed knowledge SARS-CoV-2 infection has been hampering the development treatments for coronavirus disease 2019 (COVID-19). Here, we report that RNA triggers liquid–liquid phase separation (LLPS) nucleocapsid protein, N. By analyzing all 29 proteins SARS-CoV-2, find only N is predicted as an LLPS protein. We further confirm during infection. Among 100,849 genome variants in GISAID database, identify ~37% (36,941) genomes contain a specific trio-nucleotide polymorphism...
Phase separation (PS) proteins form droplets to regulate myriad membraneless organelles (MLOs) and cellular pathways such as transcription, signaling transduction protein degeneration. PS are usually liquid-like can convert hydrogel/solid-like under certain conditions. The behavior of is regulated by co-PS partners mutations, modifications, oligomerizations, repeat regions alternative splicing the proteins. With growing interest in condensates associated proteins, we established PhaSepDB...
SRY‐box transcription factor 6 ( SOX6 ) is a member of the SOX gene family and inhibits proliferation cervical cancer cells by inducing cell cycle arrest. However, final fate significance these cell‐cycle‐arrested induced remains unclear. Here, we report that cellular senescence, which mainly mediated promoting transforming growth beta 2 TGFB2 expression subsequently activating TGFβ2–Smad2/3–p53–p21 WAF1/CIP1 –Rb pathway. promotes through MAP4K4–MAPK (JNK/ERK/p38)–ATF2 WT1–ATF2 pathways,...
Abstract Background Deletion of haploinsufficient genes or duplication triplosensitive ones results in phenotypic effects a concentration-dependent manner, and the mechanisms underlying these dosage-sensitive remain elusive. Phase separation drives functional compartmentalization biomolecules manner as well, which suggests potential link between two processes, warrants further systematic investigation. Results Here we provide bioinformatic experimental evidence to show close phase dosage...
The CRISPR/Cas9 system has become a powerful tool for molecular design breeding in livestock such as sheep. However, the efficiency of Cas9 combined with zygote microinjection remains suboptimal. In this study, mature sheep oocytes were used to assess impact various factors on editing efficiency. We found that vitro maturation is related environmental air temperature, pressure, and humidity. Our results indicate high-efficiency gene can be achieved when targeting SOCS2, DYA, TBXT, using...
Lysine acetylation is a well-studied post-translational modification on both histone and nonhistone proteins. More than 2000 acetylated proteins 4000 lysine sites have been identified by large scale mass spectrometry or traditional experimental methods. Although over 20 (K)-acetyl-transferases (KATs) characterized, which KAT responsible for given protein site mostly unknown. In this work, we collected KAT-specific manually analyzed sequence features surrounding the of substrates from three...
Liquid-liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, quantitative global analysis of chromatin LLPS property remains absent.Here, by combining chromatin-associated protein pull-down, proteomics 1,6-hexanediol (1,6-HD) treatment, we develop Hi-MS define anti-1,6-HD index (AICAP) quantify 1,6-HD sensitivity under physiological conditions....
Abstract Background Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates be degraded the ubiquitin-proteasome system. Mutations leading deregulation of degron functionality disrupt control abundance due mistargeting proteins destined for degradation and often result in pathologies. Targeting degrons small molecules also emerges as an exciting drug design strategy upregulate expression specific proteins. Despite their essential function disease...
Abstract While protein aggregation’s association with aging and age-related diseases is well-established, the specific proteins involved whether dissolving them could alleviate remain unclear. Our research addresses this gap by uncovering role of PKM2 aggregates in aging. We find that forms senescent cells organs from aged mice, impairing its enzymatic activity glycolytic flux, thereby driving into senescence. Through a rigorous two-step small molecule library screening, we identify two...
The oocyte cytoplasmic lattices (CPLs) have long been predicted to function as a storage form for the maternal contribution of ribosomes early embryo. Our previous studies demonstrated that ribosomal component S6 is stored in CPLs and peptidylarginine deiminase 6 (PADI6) critical formation. Additionally, we found depletion PADI6 reduced de novo protein synthesis prior maternal-to-embryonic transition, therefore causing embryos arrest at 2-cell stage. Here, present evidence further supporting...
Salt stress adversely impacts crop production. Several spliceosome components have been implicated in regulating salt responses plants, however, the underlying molecular basis is still unclear. Here we report that spliceosomal core protein SmEb essential to tolerance Arabidopsis. Transcriptome analysis showed modulates alternative splicing of hundreds pre-mRNAs plant response stress. Further study revealed crucial maintaining proper ratio two RCD1 variants (RCD1.1/RCD1.2) important for...
(1) Background: Litter size is one of the most important economic traits sheep. The FecB locus has been extensively studied due to its significant impact on litter in Hu sheep, and BMP15 GDF9 have also reported as major genes associated with This study aimed identify variants perform an association analysis these sheep breed. (2) Methods: In this study, exons were fully sequenced polymorphisms Population genetic parameters haplotype frequencies estimated, between polymorphic loci was...
Biomacromolecules form membraneless organelles through liquid-liquid phase separation in order to regulate the efficiency of particular biochemical reactions. Dysregulation might result pathological condensation or sequestration biomolecules, leading diseases. Thus, and separating factors may serve as drug targets for disease treatment. Nevertheless, such associations have not yet been integrated into related databases. Therefore, based on MloDisDB, a database organelle factor-disease...
A yet unidentified branched‐chain transaminase (BCAT), ApBCAT, was identified in the thermostable Aeribacillus pallidus. Notably, ApBCAT exhibits exceptional thermal stability and demonstrates ability to catalyze a wide range of natural unnatural amino acids. This combination broad substrate spectrum resistance is unusual BCAT family, indicating promising industrial potential ApBCAT.
Wnt/β-catenin signaling plays a crucial role in cancer development, primarily activated by β-catenin forming transcription complex with LEF/TCF the nucleus and initiating of Wnt target genes. Here, we report that LEF1, member family, can form intrinsically disordered region (IDR)-dependent condensates both vivo vitro, which is required for β-catenin-dependent transcription. Notably, LEF1 disrupted IDR lost its promoting activity on tumor proliferation metastasis, be restored substituting FUS...